CNE1

UniProt ID: P27825
Organism: Saccharomyces cerevisiae
Review Status: COMPLETE
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Gene 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.

Proposed New Ontology Terms

monoglucosylated glycoprotein binding

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:

Existing Annotations Review

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.

Core Functions

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.

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.
  • PMID:7814381
    Hence, Cne1p appears to function as a constituent of the S. cerevisiae ER protein quality control apparatus.
  • 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.

Cne1p recognizes monoglucosylated oligosaccharide features through its calnexin lectin site, coupling glycan recognition to ER folding and retention decisions for glycoprotein clients.

Molecular Function:
oligosaccharide binding
Directly Involved In:
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.

References

Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Expression and characterization of Saccharomyces cerevisiae Cne1p, a calnexin homologue.
  • Recombinant Cne1p shows chaperone activity and lectin-site dependence in citrate synthase denaturation/refolding assays.
    "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."
Interactions among yeast protein-disulfide isomerase proteins and endoplasmic reticulum chaperone proteins influence their activities.
  • Cne1p interacts functionally with ER oxidoreductase Mpd1p, supporting a role in the ER folding/chaperone network but not a generic protein-binding annotation.
    "Mpd1p alone does not have chaperone activity but that it interacts with and inhibits the chaperone activity of Cne1p"
Unstable mutant lysozymes are degraded through the interaction with calnexin homolog Cne1p in Saccharomyces cerevisiae.
  • Cne1p interacts with unstable misfolded lysozymes and promotes their ER retention and subsequent elimination via ER-associated degradation.
    "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."
One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy.
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.
  • Cne1p is an ER membrane glycoprotein and ER quality-control factor; the same study reported no detectable Ca2+ binding for Cne1p.
    "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."
file:yeast/CNE1/CNE1-deep-research-falcon.md
Falcon deep research report for CNE1
  • The Falcon report was reviewed and synthesized into the CNE1 curation, including core-function framing, family/PANTHER context, and evidence limitations.

Suggested Questions for Experts

Q: What are the endogenous yeast glycoprotein clients whose ER retention or ERAD depends directly on Cne1p lectin-chaperone activity?

Suggested Experiments

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

๐Ÿ“š Additional Documentation

Deep Research Falcon

(CNE1-deep-research-falcon.md)

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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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Question

Gene Research for Functional Annotation

โš ๏ธ CRITICAL: Gene/Protein Identification Context

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

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P27825
  • Protein Description: RecName: Full=Calnexin homolog; Flags: Precursor;
  • Gene Information: Name=CNE1; OrderedLocusNames=YAL058W; ORFNames=FUN48;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the calreticulin family. .
  • Key Domains: Calret/calnex. (IPR001580); Calret/calnex_CS. (IPR018124); Calreticulin/calnexin_P_dom_sf. (IPR009033); ConA-like_dom_sf. (IPR013320); Calreticulin (PF00262)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "CNE1" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

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

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol '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

Research Target:

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.

Output

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

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

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

Gene Research for Functional Annotation

โš ๏ธ CRITICAL: Gene/Protein Identification Context

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

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P27825
  • Protein Description: RecName: Full=Calnexin homolog; Flags: Precursor;
  • Gene Information: Name=CNE1; OrderedLocusNames=YAL058W; ORFNames=FUN48;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the calreticulin family. .
  • Key Domains: Calret/calnex. (IPR001580); Calret/calnex_CS. (IPR018124); Calreticulin/calnexin_P_dom_sf. (IPR009033); ConA-like_dom_sf. (IPR013320); Calreticulin (PF00262)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "CNE1" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

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

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol '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

Research Target:

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.

Research Report: Saccharomyces cerevisiae CNE1 (UniProt P27825) โ€“ Functional Annotation of the Yeast Calnexin Homolog

0) Mandatory target verification (gene/protein identity)

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)

1) Key concepts and definitions (current understanding)

1.1 Calnexin-family lectin chaperones

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)

1.2 Yeast-specific features of the โ€œcalnexin cycleโ€

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)

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

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)

2) CNE1 gene product: molecular function, binding specificity, localization, and pathway placement

2.1 Subcellular localization and membrane association

Early biochemical fractionation and microscopy established Cne1p as an ER-localized integral membrane glycoprotein.
* Cne1p is Endo Hโ€“sensitive, 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)

2.2 Calcium binding: divergence from mammalian calnexin

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)

2.3 Biochemical chaperone activity

Recombinant Cne1p exhibits molecular chaperone activity in vitro:
* A GSTโ€“Cne1p 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)

2.4 Lectin specificity for monoglucosylated N-glycans

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)

2.5 Experimentally supported client/substrate classes and outcomes (retention vs escape)

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)

2.6 Genetic/physiologic phenotypes and stress responses

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)

2.7 Interaction partners (what is supported vs not supported)

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)

3) Recent developments and latest research (prioritizing 2023โ€“2024)

3.1 Availability of 2023โ€“2024 CNE1-specific primary literature

In the retrieved corpus, direct 2023โ€“2024 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)

3.2 2022โ€“2024 synthesis relevant to CNE1 function (glycoengineering/ERQC perspective)

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)

4) Current applications and real-world implementations

Direct industrial implementations generally do not target S. cerevisiae CNE1 alone, but CNE1 is part of the engineering โ€œtoolboxโ€ for ER folding/secretory pathway tuning.

4.1 Glycoengineering and secretory pathway optimization

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)

4.2 Quality-control tuning for recombinant proteins (evidence-bearing examples)

CNE1โ€™s 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 โ€œreal-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)

5) Expert opinions and analysis (authoritative synthesis)

5.1 Expert synthesis: why CNE1 phenotypes are often subtle in budding yeast

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 calnexinโ€™s role may be narrower or โ€œone-passโ€ in budding yeast and/or more important for select substrates and stress conditions. (piirainen2022theimpactof pages 2-3, parlati1996characterizationofcalnexin pages 155-157)

5.2 Expert synthesis: glycoengineering introduces new ERQC/ERAD unknowns

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)

6) Relevant statistics and quantitative data points from retrieved studies

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 proโ€“a-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)

7) Consolidated evidence map (primary facts)

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)

9) Evidence limitations and gaps

  • 2023โ€“2024 CNE1-specific mechanistic primary literature was not prominent in the retrieved full texts; therefore, the most precise statements here rely on foundational studies plus a 2022 authoritative synthesis. (xu2004expressionandcharacterization pages 1-2, azakami2014unstablemutantlysozymes pages 1-2, piirainen2022theimpactof pages 2-3)
  • The exact endogenous client spectrum of Cne1p in budding yeast remains incompletely resolved in this evidence set; strong client evidence is available for specific heterologous/mutant substrates (lysozyme mutants, Ste2-3p reporter, ฮฑ1-antitrypsin). (azakami2014unstablemutantlysozymes pages 1-2, parlati1996characterizationofcalnexin pages 50-54)

10) Key URLs (for user convenience)

  • Xu et al., 2004 (May 2004). โ€œExpression and characterization of S. cerevisiae Cne1p, a calnexin homologue.โ€ https://doi.org/10.1093/jb/mvh074 (xu2004expressionandcharacterization pages 1-2)
  • Zhang et al., 2008 (Jan 2008). โ€œThe effect of calnexin deletion on the expression level of PDI in S. cerevisiae under heat stress conditions.โ€ https://doi.org/10.2478/s11658-007-0033-y (zhang2008theeffectof pages 1-4)
  • Azakami et al., 2014 (Jul 2014). โ€œUnstable mutant lysozymes are degraded through the interaction with calnexin homolog Cne1p in S. cerevisiae.โ€ https://doi.org/10.1080/09168451.2014.918486 (azakami2014unstablemutantlysozymes pages 1-2)
  • Piirainen & Frey, 2022 (Jun 2022). โ€œThe impact of glycoengineering on the ER quality control system in yeasts.โ€ https://doi.org/10.3389/fmolb.2022.910709 (piirainen2022theimpactof pages 2-3)
  • Rajakumar et al., 2024 (Sep 2024). โ€œDysregulation of ceramide metabolism causes phytoceramide-dependent induction of the unfolded protein response.โ€ https://doi.org/10.1091/mbc.e24-03-0121 (contextual UPR/ER homeostasis) (zhang2008theeffectof pages 1-4)

References

  1. (parlati1996characterizationofcalnexin pages 50-54): F Parlati. Characterization of calnexin in saccharomyces cerevisiae and schizosaccharomyces pombe. Unknown journal, 1996.

  2. (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.

  3. (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.

  4. (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.

  5. (parlati1996characterizationofcalnexin pages 155-157): F Parlati. Characterization of calnexin in saccharomyces cerevisiae and schizosaccharomyces pombe. Unknown journal, 1996.

  6. (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.

  7. (parlati1996characterizationofcalnexin pages 76-82): F Parlati. Characterization of calnexin in saccharomyces cerevisiae and schizosaccharomyces pombe. Unknown journal, 1996.

  8. (parlati1996characterizationofcalnexin pages 150-152): F Parlati. Characterization of calnexin in saccharomyces cerevisiae and schizosaccharomyces pombe. Unknown journal, 1996.

  9. (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.

  10. (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.

  11. (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.

  12. (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.

  13. (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.

Citations

  1. suzuki2021foldingandquality pages 8-9
  2. parlati1996characterizationofcalnexin pages 50-54
  3. parlati1996characterizationofcalnexin pages 76-82
  4. xu2004expressionandcharacterization pages 1-2
  5. azakami2014unstablemutantlysozymes pages 1-2
  6. zhang2008theeffectof pages 1-4
  7. parlati1996characterizationofcalnexin pages 150-152
  8. piirainen2022theimpactof pages 2-3
  9. parlati1996characterizationofcalnexin pages 155-157
  10. piirainen2022theimpactof pages 6-7
  11. azakami2014unstablemutantlysozymes pages 2-3
  12. piirainen2022theimpactof pages 5-6
  13. piirainen2022theimpactof pages 4-5
  14. https://doi.org/10.1093/jb/mvh074
  15. https://doi.org/10.1080/09168451.2014.918486
  16. https://doi.org/10.2478/s11658-007-0033-y
  17. https://doi.org/10.3389/fmolb.2022.910709
  18. https://doi.org/10.1091/mbc.e24-03-0121
  19. https://doi.org/10.1093/jb/mvh074;
  20. https://doi.org/10.1080/09168451.2014.918486;
  21. https://doi.org/10.2478/s11658-007-0033-y;
  22. https://doi.org/10.1093/jb/mvh074,
  23. https://doi.org/10.1016/b978-0-12-409547-2.14947-9,
  24. https://doi.org/10.3389/fmolb.2022.910709,
  25. https://doi.org/10.1080/09168451.2014.918486,
  26. https://doi.org/10.2478/s11658-007-0033-y,

๐Ÿ“„ View Raw YAML

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