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.
| 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.
|
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?
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
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-05-04T10:06:11.959231'
end_time: '2026-05-04T10:19:15.042362'
duration_seconds: 783.08
template_file: templates/gene_research_go_focused.md
template_variables:
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)
provider_config:
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citation_count: 16
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.
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
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.
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.
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.
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
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.
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.
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).
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).
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).
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).
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.
Shr3 is also implicated in promoting COPII-dependent packaging of amino acid permeases into ER-derived transport vesicles.
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).
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).
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).
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).
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).
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).
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).
While not Shr3 itself, recent work continues to develop the broader concept of substrate-specific ER accessory/chaperone proteins controlling multipass membrane cargo biogenesis:
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).
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
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
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: []