CNE1 encodes the budding yeast calnexin homolog, an ER membrane lectin chaperone of the calreticulin/calnexin family. Cne1 promotes ER protein quality control by binding glycosylated folding intermediates, assisting folding or retention of misfolded glycoproteins, and contributing to ER-associated degradation decisions. Direct biochemical evidence argues against annotating yeast Cne1 as a calcium-binding protein despite family-transfer annotations.
Definition: Binding to monoglucosylated N-linked glycan structures on glycoprotein folding intermediates in the endoplasmic reticulum.
Justification: Cne1p is a calnexin-family lectin chaperone whose relevant carbohydrate specificity is monoglucosylated glycoprotein/oligosaccharide recognition, which is more specific than broad carbohydrate binding.
Parent term: oligosaccharide binding
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0006457
protein folding
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: protein folding is a supported biological-process context for Cne1p as an ER lectin chaperone and quality-control factor.
Reason: Direct yeast evidence supports Cne1p in ER folding/quality control and retention/elimination of misfolded glycoprotein clients via ER-associated degradation.
Supporting Evidence:
PMID:25229868
These results suggest that in yeasts, Cne1p interacts with misfolded lysozyme proteins possibly causing their retention in the ER and subsequent elimination via ER-associated degradation.
file:yeast/CNE1/CNE1-deep-research-falcon.md
CNE1 (P27825) encodes Cne1p
|
|
GO:0036503
ERAD pathway
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: ERAD pathway is a supported biological-process context for Cne1p as an ER lectin chaperone and quality-control factor.
Reason: Direct yeast evidence supports Cne1p in ER folding/quality control and retention/elimination of misfolded proteins.
Supporting Evidence:
PMID:25229868
These results suggest that in yeasts, Cne1p interacts with misfolded lysozyme proteins possibly causing their retention in the ER and subsequent elimination via ER-associated degradation.
|
|
GO:0005509
calcium ion binding
|
IBA
GO_REF:0000033 |
REMOVE |
Summary: Direct Cne1p biochemical characterization did not detect Ca2+ binding, so family-transfer calcium ion binding should not be retained for yeast CNE1.
Reason: The direct yeast study contradicts the inferred calcium-binding annotation; calnexin-family membership alone is insufficient evidence for this molecular function in Cne1p.
Supporting Evidence:
PMID:7814381
Ca2+ binding activity has not been detected for Cne1p.
|
|
GO:0005789
endoplasmic reticulum membrane
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: endoplasmic reticulum membrane is supported for Cne1p, an ER membrane glycoprotein.
Reason: Direct localization and membrane-association evidence places Cne1p in the ER membrane/ER quality-control compartment.
|
|
GO:0005509
calcium ion binding
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: Direct Cne1p biochemical characterization did not detect Ca2+ binding, so family-transfer calcium ion binding should not be retained for yeast CNE1.
Reason: The direct yeast study contradicts the inferred calcium-binding annotation; calnexin-family membership alone is insufficient evidence for this molecular function in Cne1p.
Supporting Evidence:
PMID:7814381
Ca2+ binding activity has not been detected for Cne1p.
|
|
GO:0005783
endoplasmic reticulum
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: endoplasmic reticulum is supported for Cne1p, an ER membrane glycoprotein.
Reason: Direct localization and membrane-association evidence places Cne1p in the ER membrane/ER quality-control compartment.
|
|
GO:0005789
endoplasmic reticulum membrane
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: endoplasmic reticulum membrane is supported for Cne1p, an ER membrane glycoprotein.
Reason: Direct localization and membrane-association evidence places Cne1p in the ER membrane/ER quality-control compartment.
|
|
GO:0006457
protein folding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: protein folding is a supported biological-process context for Cne1p as an ER lectin chaperone and quality-control factor.
Reason: Direct yeast evidence supports Cne1p in ER folding/quality control and retention/elimination of misfolded proteins.
|
|
GO:0030246
carbohydrate binding
|
IEA
GO_REF:0000043 |
MODIFY |
Summary: CNE1 has lectin-site evidence for monoglucosylated oligosaccharide/glycoprotein recognition, so carbohydrate binding is directionally correct but too broad.
Reason: Use the more specific oligosaccharide binding term for the known calnexin lectin-site activity.
Proposed replacements:
oligosaccharide binding
Supporting Evidence:
PMID:15173200
the chaperone function of Cne1p was greatly affected in the presence of monoglucosylated oligosaccharides (G1M9) that specifically bind to the lectin site.
|
|
GO:0051082
unfolded protein binding
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: Cne1p has chaperone activity toward folding intermediates, but unfolded protein binding alone is a less informative representation of the ER lectin-chaperone function.
Reason: Replace with protein folding chaperone, while separately capturing oligosaccharide/lectin binding in core function and proposed terminology.
Proposed replacements:
protein folding chaperone
|
|
GO:0036503
ERAD pathway
|
IMP
PMID:7814381 Saccharomyces cerevisiae CNE1 encodes an endoplasmic reticul... |
ACCEPT |
Summary: ERAD pathway is supported for Cne1p through its interaction with unstable glycosylated client proteins and contribution to their ER retention/elimination.
Reason: PMID:25229868 provides direct yeast evidence that Cne1p binds unstable lysozyme mutants and contributes to their retention and elimination via ER-associated degradation.
Supporting Evidence:
PMID:25229868
These results suggest that in yeasts, Cne1p interacts with misfolded lysozyme proteins possibly causing their retention in the ER and subsequent elimination via ER-associated degradation.
|
|
GO:0005789
endoplasmic reticulum membrane
|
IDA
PMID:7814381 Saccharomyces cerevisiae CNE1 encodes an endoplasmic reticul... |
ACCEPT |
Summary: endoplasmic reticulum membrane is supported for Cne1p, an ER membrane glycoprotein.
Reason: Direct localization and membrane-association evidence places Cne1p in the ER membrane/ER quality-control compartment.
Supporting Evidence:
PMID:7814381
Localization of the Cne1p protein by differential and analytical subcellular fractionation as well as by confocal immunofluorescence microscopy showed that it was exclusively located in the endoplasmic reticulum (ER)
|
|
GO:0005783
endoplasmic reticulum
|
HDA
PMID:26928762 One library to make them all: streamlining the creation of y... |
ACCEPT |
Summary: endoplasmic reticulum is consistent with the ER biology of CNE1 and is supported by the SWAT endomembrane localization library.
Reason: Accept as supporting ER localization evidence, with gene-specific ER function anchored by the primary literature and UniProt record.
Supporting Evidence:
PMID:26928762
we constructed and investigated a library of
|
|
GO:0005515
protein binding
|
IPI
PMID:16002399 Interactions among yeast protein-disulfide isomerase protein... |
MARK AS OVER ANNOTATED |
Summary: Protein binding is too generic for the CNE1 interaction evidence with ER folding factors such as Mpd1/Eps1.
Reason: The interaction evidence is best interpreted as part of the ER chaperone/oxidoreductase quality-control network, not as a standalone generic protein-binding function.
Supporting Evidence:
PMID:16002399
Mpd1p alone does not have chaperone activity but that it interacts with and inhibits the chaperone activity of Cne1p
|
|
GO:0005515
protein binding
|
IPI
PMID:16002399 Interactions among yeast protein-disulfide isomerase protein... |
MARK AS OVER ANNOTATED |
Summary: Protein binding is too generic for the CNE1 interaction evidence with ER folding factors such as Mpd1/Eps1.
Reason: The interaction evidence is best interpreted as part of the ER chaperone/oxidoreductase quality-control network, not as a standalone generic protein-binding function.
Supporting Evidence:
PMID:16002399
Mpd1p alone does not have chaperone activity but that it interacts with and inhibits the chaperone activity of Cne1p
|
|
GO:0051082
unfolded protein binding
|
IDA
PMID:16002399 Interactions among yeast protein-disulfide isomerase protein... |
MODIFY |
Summary: Cne1p has chaperone activity toward folding intermediates, but unfolded protein binding alone is a less informative representation of the ER lectin-chaperone function.
Reason: Replace with protein folding chaperone, while separately capturing oligosaccharide/lectin binding in core function and proposed terminology.
Proposed replacements:
protein folding chaperone
Supporting Evidence:
PMID:15173200
Cne1p effectively suppressed the thermal denaturation of CS and enhanced the refolding of thermally or chemically denatured CS in a concentration-dependent manner.
|
|
GO:0006457
protein folding
|
IMP
PMID:15173200 Expression and characterization of Saccharomyces cerevisiae ... |
ACCEPT |
Summary: protein folding is a supported biological-process context for Cne1p as an ER lectin chaperone and quality-control factor.
Reason: Direct yeast evidence supports Cne1p in ER folding/quality control and retention/elimination of misfolded proteins.
Supporting Evidence:
PMID:15173200
Cne1p effectively suppressed the thermal denaturation of CS and enhanced the refolding of thermally or chemically denatured CS in a concentration-dependent manner.
|
|
GO:0051082
unfolded protein binding
|
IMP
PMID:15173200 Expression and characterization of Saccharomyces cerevisiae ... |
MODIFY |
Summary: Cne1p has chaperone activity toward folding intermediates, but unfolded protein binding alone is a less informative representation of the ER lectin-chaperone function.
Reason: Replace with protein folding chaperone, while separately capturing oligosaccharide/lectin binding in core function and proposed terminology.
Proposed replacements:
protein folding chaperone
Supporting Evidence:
PMID:15173200
Cne1p effectively suppressed the thermal denaturation of CS and enhanced the refolding of thermally or chemically denatured CS in a concentration-dependent manner.
|
Q: What are the endogenous yeast glycoprotein clients whose ER retention or ERAD depends directly on Cne1p lectin-chaperone activity?
Experiment: Use Cne1p proximity labeling or crosslinking immunoprecipitation under ER stress, with glycosylation-defective and lectin-site mutant controls, followed by quantitative client identification.
Hypothesis: Cne1p-dependent ERAD is selective for monoglucosylated glycoprotein clients rather than general unfolded proteins.
Type: proximity labeling and glycoprotein client proteomics
provider: falcon
model: Edison Scientific Literature
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start_time: '2026-05-04T10:05:17.315911'
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template_file: templates/gene_research_go_focused.md
template_variables:
organism: yeast
gene_id: CNE1
gene_symbol: CNE1
uniprot_accession: P27825
protein_description: 'RecName: Full=Calnexin homolog; Flags: Precursor;'
gene_info: Name=CNE1; OrderedLocusNames=YAL058W; ORFNames=FUN48;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the calreticulin family. .
protein_domains: Calret/calnex. (IPR001580); Calret/calnex_CS. (IPR018124); Calreticulin/calnexin_P_dom_sf.
(IPR009033); ConA-like_dom_sf. (IPR013320); Calreticulin (PF00262)
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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 'CNE1' 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 CNE1 (gene ID: CNE1, UniProt: P27825) 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 'CNE1' 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 CNE1 (gene ID: CNE1, UniProt: P27825) 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.
The UniProt accession P27825 corresponds to Saccharomyces cerevisiae (S288c) CNE1 (also YAL058W, ORF name FUN48) annotated as a calnexin homolog and member of the calreticulin/calnexin family (ER lectin chaperones). The experimental literature retrieved here consistently refers to yeast Cne1p as the S. cerevisiae calnexin homolog and ER membrane protein, matching the requested identity and organism. (parlati1996characterizationofcalnexin pages 50-54, xu2004expressionandcharacterization pages 1-2)
Calnexin (CNX) and calreticulin (CRT) are ER lectin chaperones that selectively bind monoglucosylated N-glycans on nascent glycoproteins to prevent aggregation and promote folding. CNX is typically membrane-tethered, whereas CRT is soluble. (suzuki2021foldingandquality pages 8-9)
A key conceptual difference between budding yeast and mammalian cells is reglucosylation. In organisms that encode UDP-glucose:glycoprotein glucosyltransferase (UGGT), UGGT can re-add glucose to promote repeated CNX/CRT binding; however, the review evidence indicates S. cerevisiae lacks UGGT, implying that calnexin binding may behave as a more one-pass/irreversible step in this species compared with canonical mammalian cycling. (piirainen2022theimpactof pages 2-3, parlati1996characterizationofcalnexin pages 155-157)
ERQC encompasses mechanisms that retain folding intermediates, promote productive folding, and direct terminally misfolded proteins into ERAD. In budding yeast, ERQC/ERAD decisions integrate lectin-like surveillance with glycan processing and downstream degradation pathways. (piirainen2022theimpactof pages 6-7, piirainen2022theimpactof pages 2-3)
Early biochemical fractionation and microscopy established Cne1p as an ER-localized integral membrane glycoprotein.
* Cne1p is Endo Hโsensitive, consistent with ER-type N-glycosylation. (parlati1996characterizationofcalnexin pages 50-54)
* Immunofluorescence/confocal microscopy shows Cne1p colocalizing with the ER lumenal marker Kar2p/BiP, with perinuclear and cortical ER patterns. (parlati1996characterizationofcalnexin pages 76-82)
* It is strongly membrane-associated (not extractable by typical chaotropes/high salt/carbonate used to strip peripheral proteins). (parlati1996characterizationofcalnexin pages 50-54)
Unlike mammalian calnexin, yeast Cne1p was found to be not a strong Ca2+-binding protein in ^45Ca overlay assays, and the protein lacks the mammalian-like calcium-binding capacity emphasized in other systems. (parlati1996characterizationofcalnexin pages 150-152, parlati1996characterizationofcalnexin pages 76-82)
Recombinant Cne1p exhibits molecular chaperone activity in vitro:
* A GSTโCne1p fusion protein suppressed thermal denaturation and enhanced refolding of citrate synthase in a concentration-dependent manner. (Xu et al., 2004; published May 2004; https://doi.org/10.1093/jb/mvh074) (xu2004expressionandcharacterization pages 1-2)
Cne1p shows evidence of lectin-like recognition of monoglucosylated N-glycans, consistent with calnexin-family function:
* Cne1p chaperone activity was strongly affected by a monoglucosylated oligosaccharide (reported as G1M9, consistent with Glc1Man9GlcNAc2), supporting a functional lectin site. (Xu et al., 2004; https://doi.org/10.1093/jb/mvh074) (xu2004expressionandcharacterization pages 1-2)
* In a cellular context, binding of Cne1p to misfolded glycoprotein clients was abolished by tunicamycin (inhibits N-glycosylation), supporting glycan-dependent recognition. (Azakami et al., 2014; published Jul 2014; https://doi.org/10.1080/09168451.2014.918486) (azakami2014unstablemutantlysozymes pages 1-2)
Multiple experimental systems support Cne1p as an ERQC factor that retains and promotes disposal of unstable glycoproteins:
* Misfolded/unstable glycosylated lysozyme mutants: Co-immunoprecipitation indicates Cne1p interacts with unstable glycosylated lysozyme mutants (e.g., G49N/D66H and others) and promotes their degradation/retention; cne1ฮ increases secretion and alters intracellular localization of these unstable glycoproteins, consistent with loss of ER retention. (Azakami et al., 2014; https://doi.org/10.1080/09168451.2014.918486) (azakami2014unstablemutantlysozymes pages 1-2, azakami2014unstablemutantlysozymes pages 2-3)
* Trafficking QC reporters: Deletion of CNE1 increased cell-surface expression of an ER-retained temperature-sensitive Ste2 mutant (Ste2-3p) and increased secretion of heterologous ฮฑ1-antitrypsin, consistent with reduced ERQC retention. (parlati1996characterizationofcalnexin pages 50-54, parlati1996characterizationofcalnexin pages 150-152)
CNE1 is nonessential under standard growth conditions, and loss does not necessarily produce gross growth phenotypes, indicating functional buffering by other ER folding factors. (parlati1996characterizationofcalnexin pages 50-54, zhang2008theeffectof pages 1-4)
However, deletion triggers compensatory changes consistent with ER stress buffering:
* Under heat stress (37ยฐC), a cne1ฮ strain showed increased PDI (protein disulfide isomerase) expression at mRNA and protein levels relative to wild type, while growth remained similar; the authors interpret this as compensation for loss of calnexin function. (Zhang et al., 2008; published Jan 2008; https://doi.org/10.2478/s11658-007-0033-y) (zhang2008theeffectof pages 1-4)
Evidence in the retrieved set supports two interaction categories:
1) Client interactions: direct binding to unstable glycosylated lysozyme mutants by co-IP (strong evidence). (azakami2014unstablemutantlysozymes pages 1-2)
2) Functional linkage to oxidoreductases: evidence suggests interaction/function with PDI-family members (e.g., Mpd1p in vitro; and PDI induction in cne1ฮ under heat stress), consistent with a cooperative ER folding network. (zhang2008theeffectof pages 1-4)
In contrast, early broad immunoprecipitation efforts reported difficulty detecting transient association with endogenous proteins in yeast, consistent with weak/transient interactions typical of chaperones or limitations of the assay. (parlati1996characterizationofcalnexin pages 150-152)
In the retrieved corpus, direct 2023โ2024 primary studies focused specifically on S. cerevisiae CNE1 were limited. The strongest direct mechanistic evidence available in full text here comes from foundational primary studies (1996, 2004, 2008, 2014). (parlati1996characterizationofcalnexin pages 50-54, xu2004expressionandcharacterization pages 1-2, zhang2008theeffectof pages 1-4, azakami2014unstablemutantlysozymes pages 1-2)
A 2022 review (Frontiers in Molecular Biosciences) provides a modern synthesis of how glycoengineering can perturb ERQC, including the calnexin pathway:
* It reiterates that yeast calnexin (Cne1p) binds Glc1Man9GlcNAc2, and that glucosidase-mediated glucose trimming controls release from calnexin; it emphasizes that S. cerevisiae lacks UGGT, which changes the logic of repeated binding relative to mammalian systems. (Published Jun 2022; https://doi.org/10.3389/fmolb.2022.910709) (piirainen2022theimpactof pages 2-3)
* It highlights an applied knowledge gap: many glycoengineered strains create ER N-glycans that may bypass calnexin-dependent folding or create glycans recognized by ERAD, yet the consequences for bioproduction proteins are not fully defined and may depend on the specific product. (piirainen2022theimpactof pages 5-6, piirainen2022theimpactof pages 4-5)
Although not CNE1-centric, a 2024 yeast study on UPR induction by lipid imbalance underscores that UPR can be triggered independent of obvious proteostasis defects, reinforcing the broader context in which ERQC components like Cne1 operate (i.e., not all UPR phenotypes map cleanly to classical ERAD overload). (Published Sep 2024; https://doi.org/10.1091/mbc.e24-03-0121) (zhang2008theeffectof pages 1-4)
Direct industrial implementations generally do not target S. cerevisiae CNE1 alone, but CNE1 is part of the engineering โtoolboxโ for ER folding/secretory pathway tuning.
In glycoengineered yeasts intended for biopharmaceutical production, ER glycan structures can be altered in ways that may reduce or eliminate canonical calnexin binding; this is viewed as a design constraint/unknown that can influence folding efficiency, ERAD engagement, and overall yields. (piirainen2022theimpactof pages 5-6, piirainen2022theimpactof pages 2-3)
CNE1โs role in retaining/degrading unstable glycoproteins has been exploited experimentally using heterologous model proteins:
* Unstable glycosylated lysozyme mutants are retained and degraded in a Cne1p-dependent manner; deletion increases secretion of unstable mutants, demonstrating a lever by which ERQC stringency can be altered. (Azakami et al., 2014; https://doi.org/10.1080/09168451.2014.918486) (azakami2014unstablemutantlysozymes pages 2-3, azakami2014unstablemutantlysozymes pages 1-2)
* Increased secretion of heterologous ฮฑ1-antitrypsin in a CNE1 deletion background supports the idea that manipulating CNE1 can shift the balance between retention/ERAD and export for certain recombinant proteins. (parlati1996characterizationofcalnexin pages 50-54)
These studies represent concrete โreal-worldโ implementations in research and bioprocess strain development: adjusting ERQC components such as CNE1 can change secretion of difficult-to-fold glycoproteins, but risks exporting misfolded products and/or increasing downstream quality burden. (parlati1996characterizationofcalnexin pages 50-54, azakami2014unstablemutantlysozymes pages 2-3)
A recurring interpretation is that cne1ฮ phenotypes are modest because S. cerevisiae can buffer ER folding defects through other chaperones/oxidoreductases and stress programs.
* Heat stress experiments show induction of PDI upon CNE1 deletion, consistent with a compensatory ER folding network that can preserve growth. (zhang2008theeffectof pages 1-4)
* Reviews argue that the absence of UGGT in S. cerevisiae changes the dependence on repeated calnexin binding, suggesting that calnexinโs role may be narrower or โone-passโ in budding yeast and/or more important for select substrates and stress conditions. (piirainen2022theimpactof pages 2-3, parlati1996characterizationofcalnexin pages 155-157)
The glycoengineering review emphasizes that most mechanistic ERQC evidence uses folding-deficient model substrates, and that production-relevant proteins may behave differently, sometimes not requiring glycans for folding. Nevertheless, altered ER glycans may change folding kinetics and ERAD engagement, making ERQC (including Cne1p) an important consideration in strain design. (piirainen2022theimpactof pages 5-6, piirainen2022theimpactof pages 4-5)
Because the retrieved set is dominated by mechanistic, substrate-focused studies, quantitative results are mostly presented as effect directions (e.g., increased secretion in deletion strains) rather than high-throughput statistics. Still, the following quantitative/structured points are supported:
* Sequence similarity reported in early characterization: Cne1p is ~24% identical and 31% similar to mammalian calnexin (useful for homology-based annotation but also highlights divergence). (parlati1996characterizationofcalnexin pages 50-54)
* Cne1p glycosylation shift: apparent mass shift from ~76 kDa to 60 kDa upon Endo H treatment (supporting N-glycosylation and ER residence). (parlati1996characterizationofcalnexin pages 50-54)
* ERAD-related kinetic note: degradation of unglycosylated proโa-factor in microsomes described as cytosol- and ATP-dependent with a reported ~7.5 min half-life (contextual evidence linking Cne1 to ERQC/ERAD handling of secretory substrates). (parlati1996characterizationofcalnexin pages 150-152)
The following table consolidates the strongest experimentally supported claims for functional annotation.
| Aspect | Key findings | Evidence type/method | Primary source (first author year + DOI URL) | Citation ID |
|---|---|---|---|---|
| Identity/domains | CNE1 = YAL058W/FUN48; encodes the sole S. cerevisiae calnexin/calreticulin-family homolog; ~24% identity and ~31% similarity to mammalian calnexin | Gene cloning/sequence comparison; biochemical characterization | Parlati 1996; source text unavailable for DOI in retrieved context | (parlati1996characterizationofcalnexin pages 50-54) |
| Localization/topology | ER-localized integral membrane glycoprotein; Endo H-sensitive N-glycosylation; colocalizes with Kar2/BiP; strong perinuclear and cortical ER pattern | Subcellular fractionation; carbonate/urea/high-salt extraction; Endo H shift; immunofluorescence/confocal microscopy | Parlati 1996; source text unavailable for DOI in retrieved context | (parlati1996characterizationofcalnexin pages 50-54, parlati1996characterizationofcalnexin pages 76-82) |
| Localization/topology | Contains a transmembrane region but lacks a cytoplasmic tail; deletion of TM did not fully release protein from membranes, suggesting membrane retention via protein interactions | Domain analysis; membrane association assays of truncation mutants | Parlati 1996; source text unavailable for DOI in retrieved context | (parlati1996characterizationofcalnexin pages 150-152) |
| Biochemical activity and binding specificity | Functions as a molecular chaperone; recombinant GST-Cne1p suppresses thermal aggregation and improves refolding of citrate synthase in a dose-dependent manner | In vitro thermal denaturation/refolding assay | Xu 2004; https://doi.org/10.1093/jb/mvh074 | (xu2004expressionandcharacterization pages 1-2) |
| Biochemical activity and binding specificity | Lectin-like specificity for monoglucosylated N-glycan; chaperone activity strongly affected by G1M9 oligosaccharide (Glc1Man9GlcNAc2) | Recombinant protein assay with defined oligosaccharide competitor/modulator | Xu 2004; https://doi.org/10.1093/jb/mvh074 | (xu2004expressionandcharacterization pages 1-2) |
| Biochemical activity and binding specificity | Not a strong Ca2+-binding protein; no detectable ^45Ca binding in overlay assays; unlike mammalian calnexin, lacks evident calcium-binding capacity | ^45Ca overlay; GST-fusion protein binding assay | Parlati 1996; source text unavailable for DOI in retrieved context | (parlati1996characterizationofcalnexin pages 150-152, parlati1996characterizationofcalnexin pages 76-82) |
| Substrates/clients | Binds unstable glycosylated lysozyme mutants (e.g., G49N/D66H, G49N/C76A, K13D/G49N); interaction is glycan-dependent | Co-expression and co-immunoprecipitation | Azakami 2014; https://doi.org/10.1080/09168451.2014.918486 | (azakami2014unstablemutantlysozymes pages 1-2) |
| Substrates/clients | Tunicamycin abolishes Cne1p interaction with mutant lysozymes, indicating dependence on N-linked glycosylation/lectin recognition | Tunicamycin perturbation of N-glycosylation; co-IP | Azakami 2014; https://doi.org/10.1080/09168451.2014.918486 | (azakami2014unstablemutantlysozymes pages 1-2) |
| Substrates/clients | Influences intracellular retention of misfolded cargo such as temperature-sensitive Ste2-3p and unstable glycosylated lysozyme mutants; also affects secretion of heterologous ฮฑ1-antitrypsin | Cell-surface expression assays; secretion assays; microscopy | Parlati 1996; source text unavailable for DOI in retrieved context; Azakami 2014; https://doi.org/10.1080/09168451.2014.918486 | (parlati1996characterizationofcalnexin pages 150-152, azakami2014unstablemutantlysozymes pages 2-3) |
| Phenotypes of deletion | cne1ฮ is viable and shows little or no gross defect in general growth or bulk secretion (acid phosphatase, a-factor) under standard conditions | Gene disruption; growth and secretion assays | Parlati 1996; source text unavailable for DOI in retrieved context; Zhang 2008; https://doi.org/10.2478/s11658-007-0033-y | (parlati1996characterizationofcalnexin pages 50-54, zhang2008theeffectof pages 1-4) |
| Phenotypes of deletion | cne1ฮ increases escape/secretion of unstable glycoproteins, consistent with loss of ER retention/quality control | Deletion strain comparison; secretion analysis | Xu 2004; https://doi.org/10.1093/jb/mvh074; Azakami 2014; https://doi.org/10.1080/09168451.2014.918486 | (xu2004expressionandcharacterization pages 1-2, azakami2014unstablemutantlysozymes pages 2-3) |
| Phenotypes of deletion | cne1ฮ elevates cell-surface expression of ER-retained mutant Ste2-3p and secretion of ฮฑ1-antitrypsin, supporting a QC checkpoint role | Reporter trafficking assays; heterologous secretion assays | Parlati 1996; source text unavailable for DOI in retrieved context | (parlati1996characterizationofcalnexin pages 150-152, parlati1996characterizationofcalnexin pages 50-54) |
| Phenotypes of deletion | Deletion induces compensatory ER stress responses, including increased PDI-family expression under heat stress; growth remains similar to WT at 37ยฐC | mRNA/protein expression analysis; western blot; heat-stress growth assays | Zhang 2008; https://doi.org/10.2478/s11658-007-0033-y | (zhang2008theeffectof pages 1-4) |
| Phenotypes of overexpression | Overexpression did not measurably alter general secretion of several standard reporters in early characterization studies | Overexpression strain analysis; secretion assays | Parlati 1996; source text unavailable for DOI in retrieved context | (parlati1996characterizationofcalnexin pages 150-152) |
| Interaction partners | Functional linkage with PDI-family oxidoreductases; Mpd1p reported to interact with Cne1p in vitro; PDI upregulation may compensate for Cne1 loss during stress | In vitro interaction evidence; expression response analysis | Zhang 2008; https://doi.org/10.2478/s11658-007-0033-y | (zhang2008theeffectof pages 1-4) |
| Interaction partners | Direct association demonstrated with unstable glycosylated lysozyme mutants; transient association with many endogenous cellular proteins was not detected in early studies | Co-IP for mutant clients; immunoprecipitation surveys | Azakami 2014; https://doi.org/10.1080/09168451.2014.918486; Parlati 1996; source text unavailable for DOI in retrieved context | (azakami2014unstablemutantlysozymes pages 1-2, parlati1996characterizationofcalnexin pages 150-152) |
| Pathway/process | Constituent of ER protein quality control for nascent/misfolded glycoproteins; acts as ER lectin-chaperone with weaker/modified calnexin-cycle logic because S. cerevisiae lacks UGGT-mediated reglucosylation | Integration of genetic, biochemical, and client-retention evidence | Xu 2004; https://doi.org/10.1093/jb/mvh074; Zhang 2008; https://doi.org/10.2478/s11658-007-0033-y; Parlati 1996; source text unavailable for DOI in retrieved context | (xu2004expressionandcharacterization pages 1-2, zhang2008theeffectof pages 1-4, parlati1996characterizationofcalnexin pages 155-157) |
| Pathway/process | Participates in ER retention and degradation of unstable glycoproteins, linking Cne1p to ER-associated degradation (ERAD)-related outcomes | Co-IP; glycosylation dependence; secretion/retention phenotypes in WT vs cne1ฮ | Azakami 2014; https://doi.org/10.1080/09168451.2014.918486 | (azakami2014unstablemutantlysozymes pages 1-2, azakami2014unstablemutantlysozymes pages 2-3) |
Table: This table summarizes experimentally supported facts about the budding yeast calnexin homolog CNE1/P27825, emphasizing validated localization, biochemical activity, client specificity, phenotypes, and pathway placement. It is useful as a compact evidence map for functional annotation and for distinguishing strong experimental claims from broader inference.
CNE1 (P27825) encodes Cne1p, an ER-localized integral membrane lectin chaperone of the calnexin/calreticulin family that binds monoglucosylated N-glycans (Glc1Man9GlcNAc2) and participates in ER quality control by promoting folding and/or ER retention and ERAD targeting of unstable glycoproteins. (xu2004expressionandcharacterization pages 1-2, azakami2014unstablemutantlysozymes pages 1-2, parlati1996characterizationofcalnexin pages 50-54, piirainen2022theimpactof pages 2-3)
References
(parlati1996characterizationofcalnexin pages 50-54): F Parlati. Characterization of calnexin in saccharomyces cerevisiae and schizosaccharomyces pombe. Unknown journal, 1996.
(xu2004expressionandcharacterization pages 1-2): Xiaohua Xu, Kunitoshi Kanbara, H. Azakami, and A. Kato. Expression and characterization of saccharomyces cerevisiae cne1p, a calnexin homologue. Journal of biochemistry, 135 5:615-8, May 2004. URL: https://doi.org/10.1093/jb/mvh074, doi:10.1093/jb/mvh074. This article has 49 citations and is from a peer-reviewed journal.
(suzuki2021foldingandquality pages 8-9): Tadashi Suzuki and Haruhiko Fujihira. Folding and quality control of glycoproteins. Comprehensive Glycoscience, pages 1-28, Dec 2021. URL: https://doi.org/10.1016/b978-0-12-409547-2.14947-9, doi:10.1016/b978-0-12-409547-2.14947-9. This article has 12 citations.
(piirainen2022theimpactof pages 2-3): Mari A. Piirainen and Alexander D. Frey. The impact of glycoengineering on the endoplasmic reticulum quality control system in yeasts. Frontiers in Molecular Biosciences, Jun 2022. URL: https://doi.org/10.3389/fmolb.2022.910709, doi:10.3389/fmolb.2022.910709. This article has 2 citations.
(parlati1996characterizationofcalnexin pages 155-157): F Parlati. Characterization of calnexin in saccharomyces cerevisiae and schizosaccharomyces pombe. Unknown journal, 1996.
(piirainen2022theimpactof pages 6-7): Mari A. Piirainen and Alexander D. Frey. The impact of glycoengineering on the endoplasmic reticulum quality control system in yeasts. Frontiers in Molecular Biosciences, Jun 2022. URL: https://doi.org/10.3389/fmolb.2022.910709, doi:10.3389/fmolb.2022.910709. This article has 2 citations.
(parlati1996characterizationofcalnexin pages 76-82): F Parlati. Characterization of calnexin in saccharomyces cerevisiae and schizosaccharomyces pombe. Unknown journal, 1996.
(parlati1996characterizationofcalnexin pages 150-152): F Parlati. Characterization of calnexin in saccharomyces cerevisiae and schizosaccharomyces pombe. Unknown journal, 1996.
(azakami2014unstablemutantlysozymes pages 1-2): Hiroyuki Azakami, Masayoshi Uehara, Ryohei Matsuo, Yuta Tsurunaga, Yuichiro Yamashita, Masakatsu Usui, and Akio Kato. Unstable mutant lysozymes are degraded through the interaction with calnexin homolog cne1p in saccharomyces cerevisiae. Bioscience, Biotechnology, and Biochemistry, 78:1263-1269, Jul 2014. URL: https://doi.org/10.1080/09168451.2014.918486, doi:10.1080/09168451.2014.918486. This article has 2 citations.
(azakami2014unstablemutantlysozymes pages 2-3): Hiroyuki Azakami, Masayoshi Uehara, Ryohei Matsuo, Yuta Tsurunaga, Yuichiro Yamashita, Masakatsu Usui, and Akio Kato. Unstable mutant lysozymes are degraded through the interaction with calnexin homolog cne1p in saccharomyces cerevisiae. Bioscience, Biotechnology, and Biochemistry, 78:1263-1269, Jul 2014. URL: https://doi.org/10.1080/09168451.2014.918486, doi:10.1080/09168451.2014.918486. This article has 2 citations.
(zhang2008theeffectof pages 1-4): Huili Zhang, Jianwei He, Yanyan Ji, Akio Kato, and Youtao Song. The effect of calnexin deletion on the expression level of pdi in saccharomyces cerevisiae under heat stress conditions. Cellular and Molecular Biology Letters, Jan 2008. URL: https://doi.org/10.2478/s11658-007-0033-y, doi:10.2478/s11658-007-0033-y. This article has 16 citations and is from a peer-reviewed journal.
(piirainen2022theimpactof pages 5-6): Mari A. Piirainen and Alexander D. Frey. The impact of glycoengineering on the endoplasmic reticulum quality control system in yeasts. Frontiers in Molecular Biosciences, Jun 2022. URL: https://doi.org/10.3389/fmolb.2022.910709, doi:10.3389/fmolb.2022.910709. This article has 2 citations.
(piirainen2022theimpactof pages 4-5): Mari A. Piirainen and Alexander D. Frey. The impact of glycoengineering on the endoplasmic reticulum quality control system in yeasts. Frontiers in Molecular Biosciences, Jun 2022. URL: https://doi.org/10.3389/fmolb.2022.910709, doi:10.3389/fmolb.2022.910709. This article has 2 citations.
id: P27825
gene_symbol: CNE1
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:559292
label: Saccharomyces cerevisiae
description: >-
CNE1 encodes the budding yeast calnexin homolog, an ER membrane lectin chaperone of the calreticulin/calnexin
family. Cne1 promotes ER protein quality control by binding glycosylated folding intermediates, assisting
folding or retention of misfolded glycoproteins, and contributing to ER-associated degradation decisions.
Direct biochemical evidence argues against annotating yeast Cne1 as a calcium-binding protein despite
family-transfer annotations.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- 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:15173200
title: Expression and characterization of Saccharomyces cerevisiae Cne1p, a calnexin homologue.
findings:
- statement: >-
Recombinant Cne1p shows chaperone activity and lectin-site dependence in citrate synthase denaturation/refolding
assays.
supporting_text: >-
Cne1p effectively suppressed the thermal denaturation of CS and enhanced the refolding of thermally
or chemically denatured CS in a concentration-dependent manner... the chaperone function of Cne1p
was greatly affected in the presence of monoglucosylated oligosaccharides (G1M9) that specifically
bind to the lectin site.
- id: PMID:16002399
title: >-
Interactions among yeast protein-disulfide isomerase proteins and endoplasmic reticulum chaperone
proteins influence their activities.
findings:
- statement: >-
Cne1p interacts functionally with ER oxidoreductase Mpd1p, supporting a role in the ER folding/chaperone
network but not a generic protein-binding annotation.
supporting_text: >-
Mpd1p alone does not have chaperone activity but that it interacts with and inhibits the chaperone
activity of Cne1p
- id: PMID:25229868
title: Unstable mutant lysozymes are degraded through the interaction with calnexin homolog Cne1p in Saccharomyces cerevisiae.
findings:
- statement: >-
Cne1p interacts with unstable misfolded lysozymes and promotes their ER retention and subsequent
elimination via ER-associated degradation.
supporting_text: >-
These results suggest that in yeasts, Cne1p interacts with misfolded lysozyme proteins possibly
causing their retention in the ER and subsequent elimination via ER-associated degradation.
- id: PMID:26928762
title: 'One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy.'
findings: []
- id: PMID:7814381
title: >-
Saccharomyces cerevisiae CNE1 encodes an endoplasmic reticulum (ER) membrane protein with sequence
similarity to calnexin and calreticulin and functions as a constituent of the ER quality control apparatus.
findings:
- statement: >-
Cne1p is an ER membrane glycoprotein and ER quality-control factor; the same study reported no detectable
Ca2+ binding for Cne1p.
supporting_text: >-
Localization of the Cne1p protein by differential and analytical subcellular fractionation as well
as by confocal immunofluorescence microscopy showed that it was exclusively located in the endoplasmic
reticulum (ER)... Ca2+ binding activity has not been detected for Cne1p... Hence, Cne1p appears
to function as a constituent of the S. cerevisiae ER protein quality control apparatus.
- id: file:yeast/CNE1/CNE1-deep-research-falcon.md
title: Falcon deep research report for CNE1
findings:
- statement: >-
The Falcon report was reviewed and synthesized into the CNE1 curation, including core-function framing,
family/PANTHER context, and evidence limitations.
existing_annotations:
- term:
id: GO:0006457
label: protein folding
qualifier: involved_in
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
protein folding is a supported biological-process context for Cne1p as an ER lectin chaperone and
quality-control factor.
action: ACCEPT
reason: >-
Direct yeast evidence supports Cne1p in ER folding/quality control and retention/elimination of
misfolded glycoprotein clients via ER-associated degradation.
supported_by:
- reference_id: PMID:25229868
supporting_text: >-
These results suggest that in yeasts, Cne1p interacts with misfolded lysozyme proteins possibly
causing their retention in the ER and subsequent elimination via ER-associated degradation.
reference_section_type: ABSTRACT
- reference_id: file:yeast/CNE1/CNE1-deep-research-falcon.md
supporting_text: CNE1 (P27825) encodes Cne1p
- term:
id: GO:0036503
label: ERAD pathway
qualifier: involved_in
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
ERAD pathway is a supported biological-process context for Cne1p as an ER lectin chaperone and quality-control
factor.
action: ACCEPT
reason: >-
Direct yeast evidence supports Cne1p in ER folding/quality control and retention/elimination of
misfolded proteins.
supported_by:
- reference_id: PMID:25229868
supporting_text: >-
These results suggest that in yeasts, Cne1p interacts with misfolded lysozyme proteins possibly
causing their retention in the ER and subsequent elimination via ER-associated degradation.
reference_section_type: ABSTRACT
- term:
id: GO:0005509
label: calcium ion binding
qualifier: enables
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Direct Cne1p biochemical characterization did not detect Ca2+ binding, so family-transfer calcium
ion binding should not be retained for yeast CNE1.
action: REMOVE
reason: >-
The direct yeast study contradicts the inferred calcium-binding annotation; calnexin-family membership
alone is insufficient evidence for this molecular function in Cne1p.
supported_by:
- reference_id: PMID:7814381
supporting_text: Ca2+ binding activity has not been detected for Cne1p.
reference_section_type: ABSTRACT
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
qualifier: is_active_in
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: endoplasmic reticulum membrane is supported for Cne1p, an ER membrane glycoprotein.
action: ACCEPT
reason: >-
Direct localization and membrane-association evidence places Cne1p in the ER membrane/ER quality-control
compartment.
- term:
id: GO:0005509
label: calcium ion binding
qualifier: enables
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
Direct Cne1p biochemical characterization did not detect Ca2+ binding, so family-transfer calcium
ion binding should not be retained for yeast CNE1.
action: REMOVE
reason: >-
The direct yeast study contradicts the inferred calcium-binding annotation; calnexin-family membership
alone is insufficient evidence for this molecular function in Cne1p.
supported_by:
- reference_id: PMID:7814381
supporting_text: Ca2+ binding activity has not been detected for Cne1p.
reference_section_type: ABSTRACT
- term:
id: GO:0005783
label: endoplasmic reticulum
qualifier: located_in
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: endoplasmic reticulum is supported for Cne1p, an ER membrane glycoprotein.
action: ACCEPT
reason: >-
Direct localization and membrane-association evidence places Cne1p in the ER membrane/ER quality-control
compartment.
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
qualifier: located_in
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: endoplasmic reticulum membrane is supported for Cne1p, an ER membrane glycoprotein.
action: ACCEPT
reason: >-
Direct localization and membrane-association evidence places Cne1p in the ER membrane/ER quality-control
compartment.
- term:
id: GO:0006457
label: protein folding
qualifier: involved_in
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
protein folding is a supported biological-process context for Cne1p as an ER lectin chaperone and
quality-control factor.
action: ACCEPT
reason: >-
Direct yeast evidence supports Cne1p in ER folding/quality control and retention/elimination of
misfolded proteins.
- term:
id: GO:0030246
label: carbohydrate binding
qualifier: enables
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
CNE1 has lectin-site evidence for monoglucosylated oligosaccharide/glycoprotein recognition, so
carbohydrate binding is directionally correct but too broad.
action: MODIFY
reason: Use the more specific oligosaccharide binding term for the known calnexin lectin-site activity.
proposed_replacement_terms:
- id: GO:0070492
label: oligosaccharide binding
supported_by:
- reference_id: PMID:15173200
supporting_text: >-
the chaperone function of Cne1p was greatly affected in the presence of monoglucosylated oligosaccharides
(G1M9) that specifically bind to the lectin site.
reference_section_type: ABSTRACT
- term:
id: GO:0051082
label: unfolded protein binding
qualifier: enables
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
Cne1p has chaperone activity toward folding intermediates, but unfolded protein binding alone is
a less informative representation of the ER lectin-chaperone function.
action: MODIFY
reason: >-
Replace with protein folding chaperone, while separately capturing oligosaccharide/lectin binding
in core function and proposed terminology.
proposed_replacement_terms:
- id: GO:0044183
label: protein folding chaperone
- term:
id: GO:0036503
label: ERAD pathway
qualifier: involved_in
evidence_type: IMP
original_reference_id: PMID:7814381
review:
summary: >-
ERAD pathway is supported for Cne1p through its interaction with unstable glycosylated client proteins
and contribution to their ER retention/elimination.
action: ACCEPT
reason: >-
PMID:25229868 provides direct yeast evidence that Cne1p binds unstable lysozyme mutants and contributes
to their retention and elimination via ER-associated degradation.
supported_by:
- reference_id: PMID:25229868
supporting_text: >-
These results suggest that in yeasts, Cne1p interacts with misfolded lysozyme proteins possibly
causing their retention in the ER and subsequent elimination via ER-associated degradation.
reference_section_type: ABSTRACT
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
qualifier: located_in
evidence_type: IDA
original_reference_id: PMID:7814381
review:
summary: endoplasmic reticulum membrane is supported for Cne1p, an ER membrane glycoprotein.
action: ACCEPT
reason: >-
Direct localization and membrane-association evidence places Cne1p in the ER membrane/ER quality-control
compartment.
supported_by:
- reference_id: PMID:7814381
supporting_text: >-
Localization of the Cne1p protein by differential and analytical subcellular fractionation as
well as by confocal immunofluorescence microscopy showed that it was exclusively located in the
endoplasmic reticulum (ER)
reference_section_type: ABSTRACT
- term:
id: GO:0005783
label: endoplasmic reticulum
qualifier: located_in
evidence_type: HDA
original_reference_id: PMID:26928762
review:
summary: >-
endoplasmic reticulum is consistent with the ER biology of CNE1 and is supported by the SWAT endomembrane
localization library.
action: ACCEPT
reason: >-
Accept as supporting ER localization evidence, with gene-specific ER function anchored by the primary
literature and UniProt record.
supported_by:
- reference_id: PMID:26928762
supporting_text: we constructed and investigated a library of
reference_section_type: ABSTRACT
- term:
id: GO:0005515
label: protein binding
qualifier: enables
evidence_type: IPI
original_reference_id: PMID:16002399
supporting_entities:
- SGD:S000001267
review:
summary: >-
Protein binding is too generic for the CNE1 interaction evidence with ER folding factors such as
Mpd1/Eps1.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The interaction evidence is best interpreted as part of the ER chaperone/oxidoreductase quality-control
network, not as a standalone generic protein-binding function.
supported_by:
- reference_id: PMID:16002399
supporting_text: >-
Mpd1p alone does not have chaperone activity but that it interacts with and inhibits the chaperone
activity of Cne1p
reference_section_type: ABSTRACT
- term:
id: GO:0005515
label: protein binding
qualifier: enables
evidence_type: IPI
original_reference_id: PMID:16002399
supporting_entities:
- SGD:S000005814
review:
summary: >-
Protein binding is too generic for the CNE1 interaction evidence with ER folding factors such as
Mpd1/Eps1.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The interaction evidence is best interpreted as part of the ER chaperone/oxidoreductase quality-control
network, not as a standalone generic protein-binding function.
supported_by:
- reference_id: PMID:16002399
supporting_text: >-
Mpd1p alone does not have chaperone activity but that it interacts with and inhibits the chaperone
activity of Cne1p
reference_section_type: ABSTRACT
- term:
id: GO:0051082
label: unfolded protein binding
qualifier: enables
evidence_type: IDA
original_reference_id: PMID:16002399
review:
summary: >-
Cne1p has chaperone activity toward folding intermediates, but unfolded protein binding alone is
a less informative representation of the ER lectin-chaperone function.
action: MODIFY
reason: >-
Replace with protein folding chaperone, while separately capturing oligosaccharide/lectin binding
in core function and proposed terminology.
proposed_replacement_terms:
- id: GO:0044183
label: protein folding chaperone
supported_by:
- reference_id: PMID:15173200
supporting_text: >-
Cne1p effectively suppressed the thermal denaturation of CS and enhanced the refolding of thermally
or chemically denatured CS in a concentration-dependent manner.
reference_section_type: ABSTRACT
- term:
id: GO:0006457
label: protein folding
qualifier: involved_in
evidence_type: IMP
original_reference_id: PMID:15173200
review:
summary: >-
protein folding is a supported biological-process context for Cne1p as an ER lectin chaperone and
quality-control factor.
action: ACCEPT
reason: >-
Direct yeast evidence supports Cne1p in ER folding/quality control and retention/elimination of
misfolded proteins.
supported_by:
- reference_id: PMID:15173200
supporting_text: >-
Cne1p effectively suppressed the thermal denaturation of CS and enhanced the refolding of thermally
or chemically denatured CS in a concentration-dependent manner.
reference_section_type: ABSTRACT
- term:
id: GO:0051082
label: unfolded protein binding
qualifier: enables
evidence_type: IMP
original_reference_id: PMID:15173200
review:
summary: >-
Cne1p has chaperone activity toward folding intermediates, but unfolded protein binding alone is
a less informative representation of the ER lectin-chaperone function.
action: MODIFY
reason: >-
Replace with protein folding chaperone, while separately capturing oligosaccharide/lectin binding
in core function and proposed terminology.
proposed_replacement_terms:
- id: GO:0044183
label: protein folding chaperone
supported_by:
- reference_id: PMID:15173200
supporting_text: >-
Cne1p effectively suppressed the thermal denaturation of CS and enhanced the refolding of thermally
or chemically denatured CS in a concentration-dependent manner.
reference_section_type: ABSTRACT
core_functions:
- description: >-
Cne1p is an ER membrane lectin chaperone that assists folding and quality-control retention of glycoprotein
folding intermediates. Direct studies support ER localization, chaperone activity, and contribution
to ER protein quality control/ERAD, while direct Ca2+ binding was not detected.
molecular_function:
id: GO:0044183
label: protein folding chaperone
directly_involved_in:
- id: GO:0006457
label: protein folding
- id: GO:0036503
label: ERAD pathway
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
supported_by:
- reference_id: PMID:15173200
supporting_text: >-
Cne1p effectively suppressed the thermal denaturation of CS and enhanced the refolding of thermally
or chemically denatured CS in a concentration-dependent manner.
reference_section_type: ABSTRACT
- reference_id: PMID:7814381
supporting_text: >-
Hence, Cne1p appears to function as a constituent of the S. cerevisiae ER protein quality control
apparatus.
reference_section_type: ABSTRACT
- reference_id: PMID:25229868
supporting_text: >-
These results suggest that in yeasts, Cne1p interacts with misfolded lysozyme proteins possibly
causing their retention in the ER and subsequent elimination via ER-associated degradation.
reference_section_type: ABSTRACT
- description: >-
Cne1p recognizes monoglucosylated oligosaccharide features through its calnexin lectin site, coupling
glycan recognition to ER folding and retention decisions for glycoprotein clients.
molecular_function:
id: GO:0070492
label: oligosaccharide binding
directly_involved_in:
- id: GO:0006457
label: protein folding
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
supported_by:
- reference_id: PMID:15173200
supporting_text: >-
the chaperone function of Cne1p was greatly affected in the presence of monoglucosylated oligosaccharides
(G1M9) that specifically bind to the lectin site.
reference_section_type: ABSTRACT
proposed_new_terms:
- proposed_name: monoglucosylated glycoprotein binding
proposed_definition: >-
Binding to monoglucosylated N-linked glycan structures on glycoprotein folding intermediates in the
endoplasmic reticulum.
justification: >-
Cne1p is a calnexin-family lectin chaperone whose relevant carbohydrate specificity is monoglucosylated
glycoprotein/oligosaccharide recognition, which is more specific than broad carbohydrate binding.
proposed_parent:
id: GO:0070492
label: oligosaccharide binding
supported_by:
- reference_id: PMID:15173200
supporting_text: >-
the chaperone function of Cne1p was greatly affected in the presence of monoglucosylated oligosaccharides
(G1M9) that specifically bind to the lectin site.
reference_section_type: ABSTRACT
suggested_questions:
- question: >-
What are the endogenous yeast glycoprotein clients whose ER retention or ERAD depends directly on
Cne1p lectin-chaperone activity?
suggested_experiments:
- hypothesis: >-
Cne1p-dependent ERAD is selective for monoglucosylated glycoprotein clients rather than general unfolded
proteins.
description: >-
Use Cne1p proximity labeling or crosslinking immunoprecipitation under ER stress, with glycosylation-defective
and lectin-site mutant controls, followed by quantitative client identification.
experiment_type: proximity labeling and glycoprotein client proteomics