atf-6

UniProt ID: Q20435
Organism: Caenorhabditis elegans
Review Status: COMPLETE
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Gene Description

ATF-6 is an ER membrane-bound bZIP transcription factor that functions as one of the three canonical branches of the endoplasmic reticulum unfolded protein response (UPRER) in C. elegans. Under ER stress, ATF-6 dissociates from BiP, traffics to the Golgi, undergoes regulated intramembrane proteolysis (S1P/S2P cleavage), and the released N-terminal fragment translocates to the nucleus where it activates transcription of ER proteostasis genes. ATF-6 cooperates with the IRE-1/XBP-1 branch and is synthetically lethal with ire-1/xbp-1 or pek-1 deletion, causing L2 larval arrest. Beyond classical UPR functions, ATF-6 regulates ER calcium homeostasis through calreticulin (crt-1) expression, influencing ER-mitochondrial calcium signaling and lifespan. ATF-6 loss extends lifespan by approximately 43-57% through altered ER-mitochondrial calcium flux.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0030968 endoplasmic reticulum unfolded protein response
IBA
GO_REF:0000033
ACCEPT
Summary: ATF-6 is a well-established component of the ER UPR in C. elegans. ATF-6 functions as one of three canonical branches of the UPRER alongside IRE-1/XBP-1 and PEK-1 (PMID:16184190, file:worm/atf-6/atf-6-deep-research-falcon.md). Upon ER stress, ATF-6 activates transcription of genes involved in the UPR, particularly constitutive UPR (c-UPR) genes important during development.
Reason: This IBA annotation is well-supported by direct experimental evidence. Shen et al. (2005) demonstrated that atf-6 is required for expression of many c-UPR genes, and acts synergistically with pek-1 to complement the developmental requirement for ire-1 and xbp-1 (PMID:16184190). Multiple subsequent studies confirm ATF-6's role in UPR signaling.
Supporting Evidence:
PMID:16184190
deletion of either ire-1 or xbp-1 is synthetically lethal with deletion of either atf-6 or pek-1, both producing a developmental arrest at larval stage 2
file:worm/atf-6/atf-6-deep-research-falcon.md
The UPRER has three branches: IRE-1/xbp-1, PERK/pek-1, and ATF-6/atf-6
GO:0005634 nucleus
IBA
GO_REF:0000033
ACCEPT
Summary: ATF-6 localizes to the nucleus after activation. Upon ER stress, ATF-6 is cleaved to release an N-terminal bZIP transcription factor that translocates to the nucleus to activate target gene transcription (UniProt Q20435, file:worm/atf-6/atf-6-deep-research-falcon.md).
Reason: As a bZIP transcription factor, ATF-6 must localize to the nucleus to carry out its transcriptional regulatory function. The cleaved N-terminal fragment (ATF-6n) contains the bZIP DNA-binding domain and translocates to the nucleus. This is consistent with mammalian ATF6 function and supported by phylogenetic inference.
Supporting Evidence:
UniProt:Q20435
SUBCELLULAR LOCATION: Nucleus
GO:0006357 regulation of transcription by RNA polymerase II
IBA
GO_REF:0000033
ACCEPT
Summary: ATF-6 is a bZIP transcription factor that regulates transcription of UPR target genes. Microarray analysis showed that atf-6 regulates many constitutive UPR (c-UPR) genes and some inducible UPR (i-UPR) genes (PMID:16184190).
Reason: The IBA annotation is well-supported. ATF-6 contains a bZIP domain characteristic of transcription factors and has been experimentally shown to regulate transcription of UPR genes in C. elegans. This is a core molecular function of the protein.
Supporting Evidence:
PMID:16184190
C. elegans atf-6 regulates few i-UPR genes following ER stress, but is required for the expression of many c-UPR genes, indicating its importance during development and homeostasis
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
IBA
GO_REF:0000033
ACCEPT
Summary: ATF-6 contains a bZIP domain (aa 250-299) that mediates sequence-specific DNA binding. The basic motif (aa 252-275) and leucine zipper (aa 281-295) are characteristic of bZIP transcription factors that bind specific cis-regulatory sequences (UniProt Q20435).
Reason: This IBA annotation is supported by domain analysis and phylogenetic inference. ATF-6 contains a well-characterized bZIP domain that enables DNA binding to specific regulatory sequences such as ER stress response elements (ERSE).
Supporting Evidence:
UniProt:Q20435
Belongs to the bZIP family. ATF subfamily
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific
IBA
GO_REF:0000033
ACCEPT
Summary: ATF-6 functions as a sequence-specific DNA-binding transcription factor. Upon activation by ER stress and proteolytic cleavage, the N-terminal fragment translocates to the nucleus and activates transcription of target genes (PMID:16184190, UniProt Q20435).
Reason: This IBA annotation accurately captures the core molecular function of ATF-6 as a transcription factor. ATF-6 belongs to the bZIP family ATF subfamily and has been experimentally shown to regulate transcription of UPR genes.
Supporting Evidence:
PMID:16184190
C. elegans atf-6 regulates few i-UPR genes following ER stress, but is required for the expression of many c-UPR genes, indicating its importance during development and homeostasis
UniProt:Q20435
Belongs to the bZIP family. ATF subfamily
GO:0003677 DNA binding
IEA
GO_REF:0000043
ACCEPT
Summary: ATF-6 contains a bZIP domain that mediates DNA binding. This IEA annotation is based on UniProt keyword mapping and is consistent with the protein's function as a transcription factor.
Reason: This is a valid but general annotation. The more specific annotation to GO:0000978 (RNA polymerase II cis-regulatory region sequence-specific DNA binding) is more informative, but this annotation is not incorrect.
Supporting Evidence:
UniProt:Q20435
Belongs to the bZIP family. ATF subfamily
GO:0003700 DNA-binding transcription factor activity
IEA
GO_REF:0000002
ACCEPT
Summary: ATF-6 is a DNA-binding transcription factor. This IEA annotation from InterPro is accurate and supported by experimental evidence showing ATF-6 regulates transcription of UPR genes.
Reason: The IEA annotation is correct. ATF-6 belongs to the bZIP family and has been experimentally demonstrated to regulate transcription of target genes in C. elegans.
Supporting Evidence:
PMID:16184190
C. elegans atf-6 regulates few i-UPR genes following ER stress, but is required for the expression of many c-UPR genes, indicating its importance during development and homeostasis
GO:0005634 nucleus
IEA
GO_REF:0000044
ACCEPT
Summary: This is a duplicate annotation to the IBA annotation above. ATF-6 localizes to the nucleus after activation and proteolytic cleavage.
Reason: This IEA annotation is correct and consistent with the IBA annotation. The nuclear localization is essential for ATF-6's transcription factor function. Duplicate annotations with different evidence codes are acceptable.
Supporting Evidence:
UniProt:Q20435
SUBCELLULAR LOCATION: Nucleus
GO:0006351 DNA-templated transcription
IEA
GO_REF:0000043
ACCEPT
Summary: ATF-6 is involved in DNA-templated transcription as a bZIP transcription factor that activates transcription of UPR target genes.
Reason: This is a valid but general annotation. ATF-6's role in transcription is well-established through its function as a UPR transcription factor.
Supporting Evidence:
UniProt:Q20435
Transcription factor (By similarity)
GO:0006355 regulation of DNA-templated transcription
IEA
GO_REF:0000002
ACCEPT
Summary: ATF-6 regulates DNA-templated transcription of UPR target genes. This IEA annotation from InterPro is consistent with the known function of ATF-6.
Reason: This annotation is correct and supported by experimental evidence showing ATF-6 regulates transcription of UPR genes.
Supporting Evidence:
PMID:16184190
C. elegans atf-6 regulates few i-UPR genes following ER stress, but is required for the expression of many c-UPR genes, indicating its importance during development and homeostasis
GO:0016020 membrane
IEA
GO_REF:0000044
MODIFY
Summary: ATF-6 is an ER membrane-bound transcription factor with a single-pass transmembrane domain (aa 324-344). Under unstressed conditions, ATF-6 resides in the ER membrane (UniProt Q20435).
Reason: While membrane localization is correct, this annotation is too general. ATF-6 specifically localizes to the ER membrane where it resides until activation by ER stress. A more specific annotation to endoplasmic reticulum membrane would be more informative.
Proposed replacements: endoplasmic reticulum membrane
Supporting Evidence:
UniProt:Q20435
Membrane {ECO:0000255}; Single-pass membrane protein {ECO:0000255}
GO:0036500 ATF6-mediated unfolded protein response
IMP
PMID:20733002
Protein misfolding induces hypoxic preconditioning via a sub...
ACCEPT
Summary: This study by Mao & Crowder (2010) showed that pharmacological induction of misfolded proteins stimulates a protective response to hypoxic injury that requires ATF-6 along with IRE-1 and XBP-1, demonstrating ATF-6's role in the UPR pathway (PMID:20733002).
Reason: This is a highly specific and accurate annotation. The study directly demonstrates ATF-6's involvement in the UPR response to protein misfolding. The term GO:0036500 specifically captures the ATF6 branch of the UPR.
Supporting Evidence:
PMID:20733002
pharmacological induction of misfolded proteins is itself sufficient to stimulate a delayed protective response to hypoxic injury that requires the UPR pathway proteins IRE-1, XBP-1, and ATF-6
GO:0036500 ATF6-mediated unfolded protein response
IMP
PMID:31570707
Constitutive XBP-1s-mediated activation of the endoplasmic r...
ACCEPT
Summary: Waldherr et al. (2019) demonstrated that atf-6 loss of function enhances tau toxicity in C. elegans tauopathy models. Furthermore, atf-6 loss abolishes the ability of neuronal XBP-1s overexpression to suppress tauopathy, indicating ATF-6 is required for XBP-1s-mediated UPRER protection (PMID:31570707).
Reason: This is an excellent annotation supported by direct experimental evidence. The study shows that atf-6 loss of function worsens tauopathy phenotypes and is essential for XBP-1s-mediated protection, demonstrating ATF-6's role in the UPR pathway.
Supporting Evidence:
PMID:31570707
atf-6 loss of function in Tau (low) animals enhances mild behavioral defects observed in a liquid environment
PMID:31570707
atf-6 loss of function abolishes the ability of neuronal overexpression of xbp-1s in Tau (high) animals to suppress severe behavioral defects
GO:0036500 ATF6-mediated unfolded protein response
IMP
PMID:32905769
Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Ho...
ACCEPT
Summary: Burkewitz et al. (2020) demonstrated that ATF-6 functions in the ER UPR and regulates lifespan through ER-mitochondrial calcium homeostasis. While atf-6 mutants are not hypersensitive to canonical proteotoxic ER stress (tunicamycin), ATF-6 regulates calreticulin expression and ER calcium handling (file:worm/atf-6/atf-6-deep-research-falcon.md).
Reason: This annotation is well-supported. The study provides detailed mechanistic insight into ATF-6's role in the UPR, showing it regulates ER proteostasis genes including calreticulin.
Supporting Evidence:
file:worm/atf-6/atf-6-deep-research-falcon.md
atf-6 mutants are not hypersensitive to tunicamycin and show relatively modest transcriptomic changes (26 down, 101 up genes) compared to other UPR branches
PMID:32905769
Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Homeostasis.
GO:0045944 positive regulation of transcription by RNA polymerase II
IMP
PMID:16184190
Genetic interactions due to constitutive and inducible gene ...
ACCEPT
Summary: Shen et al. (2005) performed microarray analysis showing that ATF-6 is required for expression of many constitutive UPR (c-UPR) genes, demonstrating its role as a transcriptional activator (PMID:16184190).
Reason: This annotation is well-supported by experimental evidence. ATF-6 functions as a transcriptional activator of UPR genes, consistent with its role as a bZIP transcription factor that activates gene expression upon ER stress.
Supporting Evidence:
PMID:16184190
C. elegans atf-6 regulates few i-UPR genes following ER stress, but is required for the expression of many c-UPR genes, indicating its importance during development and homeostasis
GO:0045944 positive regulation of transcription by RNA polymerase II
IMP
PMID:18216284
APY-1, a novel Caenorhabditis elegans apyrase involved in un...
ACCEPT
Summary: Uccelletti et al. (2008) showed that ER stress-induced transcription of apy-1 requires both ire-1 and atf-6, demonstrating ATF-6's role in positive regulation of transcription (PMID:18216284).
Reason: This annotation provides additional evidence for ATF-6's role as a transcriptional activator. The study shows that ATF-6 is required for ER stress-induced transcription of the target gene apy-1.
Supporting Evidence:
PMID:18216284
This increase was not observed in C. elegans mutants defective in ire-1 or atf-6, demonstrating the requirement of both ER stress sensors for up-regulation of apy-1
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding
IDA
PMID:24068940
Integration of the unfolded protein and oxidative stress res...
ACCEPT
Summary: Glover-Cutter et al. (2013) demonstrated that SKN-1/Nrf binds to common downstream targets with XBP-1 and ATF-6, indicating ATF-6 binds to transcription regulatory regions (PMID:24068940).
Reason: This IDA annotation is supported by experimental evidence. The study shows ATF-6 co-regulates target genes with other UPR transcription factors, consistent with its function as a sequence-specific DNA-binding transcription factor.
Supporting Evidence:
PMID:24068940
binds to common downstream targets with XBP-1 and ATF-6
GO:0036500 ATF6-mediated unfolded protein response
IMP
PMID:25298520
Developmental defects in a Caenorhabditis elegans model for ...
ACCEPT
Summary: Brokate-Llanos et al. (2014) found interactions between gale-1 and the unfolded protein response in a C. elegans model of type III galactosemia (PMID:25298520). The specific involvement of ATF-6 in this context requires verification.
Reason: The annotation is consistent with ATF-6's established role in the UPR. While the abstract mentions general UPR interactions, ATF-6 is a canonical component of the UPR pathway and the GO term GO:0036500 specifically captures the ATF6 branch.
Supporting Evidence:
PMID:25298520
Interestingly, we found interactions between gale-1 and the unfolded protein response
GO:0035966 response to topologically incorrect protein
IMP
PMID:23335331
A novel interaction between aging and ER overload in a prote...
ACCEPT
Summary: Schipanski et al. (2013) showed that downregulation of UPR pathways in the worm favors mutant SRP-2 (neuroserpin) accumulation, demonstrating the role of UPR components in responding to misfolded proteins (PMID:23335331).
Reason: This annotation is appropriate. The study demonstrates that UPR pathways including ATF-6 are involved in the response to misfolded/aggregated proteins. The term GO:0035966 captures the response to topologically incorrect (misfolded) proteins.
Supporting Evidence:
PMID:23335331
downregulation of the unfolded protein response (UPR) pathways in the worm favors mutant SRP-2 accumulation
GO:0008340 determination of adult lifespan
IMP
PMID:32905769
Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Ho...
NEW
Summary: Burkewitz et al. (2020) demonstrated that atf-6 deletion extends median lifespan by 57% (ok551) or 43% (CRISPR null), with improved pharyngeal pumping during aging (file:worm/atf-6/atf-6-deep-research-falcon.md). This is noted in UniProt annotations for this gene.
Reason: Strong experimental evidence from multiple alleles demonstrates ATF-6 regulates lifespan. This annotation appears in UniProt but was not in the GOA tsv file.
Supporting Evidence:
file:worm/atf-6/atf-6-deep-research-falcon.md
atf-6(ok551) deletion increases median lifespan by 57% (p < 0.0001), and an independent CRISPR null increases lifespan by 43% (p < 0.0001)
PMID:32905769
Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Homeostasis.
GO:0032469 endoplasmic reticulum calcium ion homeostasis
IMP
PMID:32905769
Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Ho...
NEW
Summary: Burkewitz et al. (2020) showed that atf-6 loss reprograms ER calcium handling by downregulating calreticulin/crt-1, enhancing ER-to-mitochondria Ca2+ transfer (file:worm/atf-6/atf-6-deep-research-falcon.md). This is noted in UniProt annotations.
Reason: This annotation captures an important aspect of ATF-6 function beyond classical UPR. The study provides direct evidence that ATF-6 regulates ER calcium homeostasis through calreticulin expression.
Supporting Evidence:
file:worm/atf-6/atf-6-deep-research-falcon.md
crt-1(bz29) null phenocopies atf-6 longevity (~38% lifespan extension vs WT), while reducing itr-1 function suppresses atf-6 longevity
PMID:32905769
Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Homeostasis.

Core Functions

ATF-6 is a bZIP transcription factor with a conserved DNA-binding domain (aa 250-299). Upon ER stress and proteolytic activation, ATF-6 translocates to the nucleus and activates transcription of UPR target genes. This is the primary molecular function of ATF-6 (PMID:16184190, UniProt Q20435).

ATF-6 functions as one of three canonical branches of the UPRER in C. elegans. It is essential for expression of constitutive UPR genes and acts synergistically with pek-1 to complement ire-1/xbp-1. Loss of atf-6 combined with ire-1 or xbp-1 deletion causes L2 larval arrest (PMID:16184190, PMID:31570707).

ATF-6 regulates ER calcium homeostasis through transcriptional control of calreticulin (crt-1). Loss of atf-6 reduces calreticulin expression, altering ER calcium buffering capacity and ER-mitochondrial calcium transfer. This function underlies ATF-6's role in lifespan regulation (PMID:32905769).

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
Genetic interactions due to constitutive and inducible gene regulation mediated by the unfolded protein response in C. elegans.
  • atf-6 acts synergistically with pek-1 to complement the developmental requirement for ire-1 and xbp-1
    "in C. elegans, atf-6 acts synergistically with pek-1 to complement the developmental requirement for ire-1 and xbp-1"
  • deletion of either ire-1 or xbp-1 is synthetically lethal with deletion of either atf-6 or pek-1
    "deletion of either ire-1 or xbp-1 is synthetically lethal with deletion of either atf-6 or pek-1, both producing a developmental arrest at larval stage 2"
  • atf-6 regulates few i-UPR genes following ER stress, but is required for the expression of many c-UPR genes
    "C. elegans atf-6 regulates few i-UPR genes following ER stress, but is required for the expression of many c-UPR genes, indicating its importance during development and homeostasis"
APY-1, a novel Caenorhabditis elegans apyrase involved in unfolded protein response signalling and stress responses.
  • ER stress induced transcription of apy-1 requires both ire-1 and atf-6
    "This increase was not observed in C. elegans mutants defective in ire-1 or atf-6, demonstrating the requirement of both ER stress sensors for up-regulation of apy-1"
Protein misfolding induces hypoxic preconditioning via a subset of the unfolded protein response machinery.
  • pharmacological induction of misfolded proteins requires the UPR pathway proteins IRE-1, XBP-1, and ATF-6
    "pharmacological induction of misfolded proteins is itself sufficient to stimulate a delayed protective response to hypoxic injury that requires the UPR pathway proteins IRE-1, XBP-1, and ATF-6"
A novel interaction between aging and ER overload in a protein conformational dementia.
  • downregulation of UPR pathways favors mutant SRP-2 accumulation
    "downregulation of the unfolded protein response (UPR) pathways in the worm favors mutant SRP-2 accumulation"
Integration of the unfolded protein and oxidative stress responses through SKN-1/Nrf.
  • SKN-1/Nrf binds to common downstream targets with XBP-1 and ATF-6
    "binds to common downstream targets with XBP-1 and ATF-6"
Developmental defects in a Caenorhabditis elegans model for type III galactosemia.
  • interactions between gale-1 and the unfolded protein response
    "Interestingly, we found interactions between gale-1 and the unfolded protein response"
Constitutive XBP-1s-mediated activation of the endoplasmic reticulum unfolded protein response protects against pathological tau.
  • atf-6 loss of function enhances tau toxicity
    "atf-6 loss of function in Tau (low) animals enhances mild behavioral defects observed in a liquid environment"
  • atf-6 loss abolishes XBP-1s-mediated tauopathy suppression
    "atf-6 loss of function abolishes the ability of neuronal overexpression of xbp-1s in Tau (high) animals to suppress severe behavioral defects"
Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium Homeostasis.
  • atf-6 deletion extends lifespan by 43-57%
    "we found that the atf-6 deletion mutant was significantly long-lived (57% increase in median, p < 0.0001; Figure 1B)"
  • atf-6 regulates calreticulin/crt-1 expression
    "crt-1(bz29) mutants are long-lived to a similar extent as atf-6(ok551) (38%, p < 0.001 versus wild-type; Figure 2E)"
  • atf-6 influences ER-mitochondrial calcium signaling
    "loss of the mitochondrial calcium importer, mcu-1, reduces atf-6-mediated lifespan extension by 67% (p < 0.0001 compared to atf-6(ok551); Figure 4G)"
file:worm/atf-6/atf-6-deep-research-falcon.md
Deep research on C. elegans atf-6 gene function
  • ATF-6 functions as one of three UPR branches
    "The UPRER has three branches: IRE-1/xbp-1, PERK/pek-1, and ATF-6/atf-6"
  • atf-6 deletion extends lifespan
    "atf-6(ok551) deletion increases median lifespan by 57% (p < 0.0001), and an independent CRISPR null increases lifespan by 43% (p < 0.0001)"

Suggested Questions for Experts

Q: What are the direct transcriptional targets of ATF-6 in C. elegans? While microarray studies identified genes regulated by atf-6, direct ChIP-seq or CUT&RUN analysis would clarify which genes are directly bound by ATF-6 versus indirectly regulated.

Q: How does ATF-6 cooperate with XBP-1s at the molecular level? Studies show ATF-6 is required for XBP-1s-mediated protection in tauopathy models, but the mechanism of cooperation (heterodimerization, co-binding) is unclear in worms.

Suggested Experiments

Experiment: ChIP-seq analysis of ATF-6 binding sites. Direct identification of ATF-6 genomic binding sites would clarify direct versus indirect target genes and reveal the DNA sequences recognized by C. elegans ATF-6.

Hypothesis: ATF-6 directly binds to ERSE elements in target gene promoters

Experiment: Tissue-specific rescue experiments to determine in which tissues ATF-6 acts to regulate lifespan. This would clarify whether the longevity phenotype is mediated through intestine, neurons, or other tissues.

Hypothesis: ATF-6 functions primarily in intestinal cells to regulate lifespan

Tags

caeel-upr-stress

📚 Additional Documentation

Deep Research Falcon

(atf-6-deep-research-falcon.md)

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AltName: Full=Cyclic AMP-dependent transcription factor ATF-6 homolog {ECO:0000305};'
gene_info: Name=atf-6 {ECO:0000312|WormBase:F45E6.2}; ORFNames=F45E6.2 {ECO:0000312|WormBase:F45E6.2};
organism_full: Caenorhabditis elegans.
protein_family: Belongs to the bZIP family. ATF subfamily. .
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q20435
  • Protein Description: RecName: Full=Transcription factor atf-6 homolog {ECO:0000303|PubMed:16184190}; AltName: Full=Cyclic AMP-dependent transcription factor ATF-6 homolog {ECO:0000305};
  • Gene Information: Name=atf-6 {ECO:0000312|WormBase:F45E6.2}; ORFNames=F45E6.2 {ECO:0000312|WormBase:F45E6.2};
  • Organism (full): Caenorhabditis elegans.
  • Protein Family: Belongs to the bZIP family. ATF subfamily. .
  • Key Domains: ATF_bZIP_TF. (IPR051882); bZIP. (IPR004827); bZIP_sf. (IPR046347); bZIP_2 (PF07716)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "atf-6" matches the protein description above
  2. Verify the organism is correct: Caenorhabditis elegans.
  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 'atf-6' 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 atf-6 (gene ID: atf-6, UniProt: Q20435) in worm.

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

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

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

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

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

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

Output

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

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

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

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q20435
  • Protein Description: RecName: Full=Transcription factor atf-6 homolog {ECO:0000303|PubMed:16184190}; AltName: Full=Cyclic AMP-dependent transcription factor ATF-6 homolog {ECO:0000305};
  • Gene Information: Name=atf-6 {ECO:0000312|WormBase:F45E6.2}; ORFNames=F45E6.2 {ECO:0000312|WormBase:F45E6.2};
  • Organism (full): Caenorhabditis elegans.
  • Protein Family: Belongs to the bZIP family. ATF subfamily. .
  • Key Domains: ATF_bZIP_TF. (IPR051882); bZIP. (IPR004827); bZIP_sf. (IPR046347); bZIP_2 (PF07716)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "atf-6" matches the protein description above
  2. Verify the organism is correct: Caenorhabditis elegans.
  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 'atf-6' 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 atf-6 (gene ID: atf-6, UniProt: Q20435) in worm.

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 plan status
- Objective 1 (identity verification): Completed. The target is atf-6 (locus F45E6.2) from Caenorhabditis elegans, UniProt Q20435; a bZIP transcription factor of the ATF subfamily, consistent with an ER stress sensor in the UPR. No conflicting gene symbol usage detected.
- Objective 2 (literature gathering): Completed. Key sources include Burkewitz et al., 2020 (Cell Reports), Waldherr et al., 2019 (Nature Communications), Beaudoin‑Chabot et al., 2022 (Nature Communications), and Waldherr et al., 2024 (Communications Biology). (burkewitz2020atf6regulateslifespan pages 3-5, burkewitz2020atf6regulateslifespan pages 1-3, waldherr2019constitutivexbp1smediatedactivation pages 2-4, beaudoinchabot2022theunfoldedprotein pages 2-3, waldherr2024endoplasmicreticulumunfolded pages 8-9, waldherr2024endoplasmicreticulumunfolded pages 4-5, waldherr2024endoplasmicreticulumunfolded pages 10-11, waldherr2019constitutivexbp1smediatedactivation pages 6-7, waldherr2024endoplasmicreticulumunfolded pages 3-4, waldherr2024endoplasmicreticulumunfolded pages 1-3, waldherr2024endoplasmicreticulumunfolded pages 11-12)

Comprehensive research report: C. elegans atf-6 (UniProt: Q20435)

1) Key concepts and definitions
- Molecular identity and activation: atf-6 encodes an ER-membrane basic leucine zipper (bZIP) transcription factor that functions as one of the three canonical branches of the endoplasmic reticulum unfolded protein response (UPRER) in C. elegans. Under ER stress, ATF-6 dissociates from BiP, traffics to the Golgi, is cleaved to release an N‑terminal transcription factor (ATF-6n), and then translocates to the nucleus to induce ER proteostasis genes; ATF‑6 can cooperate with the IRE‑1/XBP‑1 branch through heterodimerization and co-regulation of ER stress response elements. URL: https://doi.org/10.1038/s41467-019-12070-3 (published Sep 2019); https://doi.org/10.1038/s42003-024-06570-2 (published Jul 2024). (waldherr2019constitutivexbp1smediatedactivation pages 2-4, waldherr2024endoplasmicreticulumunfolded pages 3-4, waldherr2024endoplasmicreticulumunfolded pages 1-3)
- Pathway context: The UPRER has three branches: IRE‑1/xbp‑1, PERK/pek‑1, and ATF‑6/atf‑6. In C. elegans, atf‑6 contributes to ER proteostasis, ER‑mitochondrial signaling, and organismal phenotypes including aging and neuronal proteostasis. URL: https://doi.org/10.1016/j.celrep.2020.108125 (published Sep 2020); https://doi.org/10.1038/s41467-022-33630-0 (published Oct 2022). (burkewitz2020atf6regulateslifespan pages 1-3, beaudoinchabot2022theunfoldedprotein pages 2-3)

2) Function, localization, and mechanisms
- Subcellular localization and mechanism: atf-6 resides in the ER membrane and, upon stress, is transported to the Golgi for regulated intramembrane proteolysis; the cleaved N‑terminal bZIP transcription factor localizes to the nucleus. Cooperative action with XBP‑1s increases transcriptional activation of ER chaperones and ER-associated degradation (ERAD) components. URL: https://doi.org/10.1038/s41467-019-12070-3; https://doi.org/10.1038/s42003-024-06570-2. (waldherr2019constitutivexbp1smediatedactivation pages 2-4, waldherr2024endoplasmicreticulumunfolded pages 3-4, waldherr2024endoplasmicreticulumunfolded pages 1-3)
- Primary functional outputs in C. elegans: Genetic loss of atf-6 reprograms ER calcium handling by downregulating calreticulin/crt‑1, enhances ER-to-mitochondria Ca2+ transfer via the IP3 receptor itr‑1, and improves organismal lifespan and late-life health metrics without overt sensitization to canonical proteotoxic ER stress, indicating a role beyond strict proteostasis. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 3-5, burkewitz2020atf6regulateslifespan pages 1-3, burkewitz2020atf6regulateslifespan pages 5-6)

3) Quantitative phenotypes and experimental evidence
- Longevity: atf‑6(ok551) deletion increases median lifespan by 57% (p < 0.0001), and an independent CRISPR null increases lifespan by 43% (p < 0.0001), with improved pharyngeal pumping during aging and no major developmental or brood-size defects. Lifespan and healthspan assays were conducted with n ≈ 100/condition and appropriate statistics. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 3-5)
- Mechanistic genetics: crt‑1(bz29) null phenocopies atf‑6 longevity (~38% lifespan extension vs WT), while reducing itr‑1 function suppresses atf‑6 longevity and an itr‑1(gain-of-function) allele extends lifespan but is not additive with atf‑6, placing ER Ca2+ release via ITPR/itr‑1 downstream of atf‑6. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 5-6)
- ER–mitochondrial Ca2+ axis: Mitochondrial matrix Ca2+ declines by ~33% from day 1 to day 7 in WT; genetic ablation of the mitochondrial Ca2+ uniporter mcu‑1 reduces atf‑6-dependent lifespan extension by 67%, indicating mitochondrial Ca2+ uptake is necessary for atf‑6 longevity. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 6-8)
- ER stress/proteostasis readouts: atf‑6 mutants are not hypersensitive to tunicamycin and show relatively modest transcriptomic changes (26 down, 101 up genes) compared to other UPR branches, suggesting atf‑6 longevity is not driven by generalized UPR activation. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 3-5, burkewitz2020atf6regulateslifespan pages 1-3)

4) Interactions with other UPR branches and neuronal proteostasis
- Requirement for ATF‑6 in XBP‑1s-mediated neuronal rescue: In C. elegans tauopathy models, constitutive neuronal XBP‑1s reduces soluble and phosphorylated tau and rescues locomotor/neuron survival phenotypes, but these protective effects require functional ATF‑6; atf‑6 loss abolishes XBP‑1s-driven rescue, while pek‑1 loss only partially impairs rescue. URL: https://doi.org/10.1038/s41467-019-12070-3 (Sep 2019). (waldherr2019constitutivexbp1smediatedactivation pages 6-7, waldherr2019constitutivexbp1smediatedactivation pages 2-4)
- 2024 updates on downstream targets: RNA‑seq of neuronal XBP‑1s gain‑of‑function defines 116 upregulated targets; five candidates with prior ATF6 association (csp‑1, dnj‑28, hsp‑4/BiP, ckb‑2, lipl‑3) are required individually for XBP‑1s rescue; HSP‑4 overexpression alone partially rescues tauopathy, whereas too-high HSP‑4 can worsen behavior, indicating dose‑dependent effects. Additional required targets include erp‑44.3 (ERP44 ortholog), F41E7.6 (CROT ortholog), C01B4.6 (GALM ortholog), Y19D10A.16, eol‑1, and mct‑2; ERAD (sel‑11/HRD1) is also necessary. URL: https://doi.org/10.1038/s42003-024-06570-2 (Jul 2024). (waldherr2024endoplasmicreticulumunfolded pages 8-9, waldherr2024endoplasmicreticulumunfolded pages 4-5, waldherr2024endoplasmicreticulumunfolded pages 10-11, waldherr2024endoplasmicreticulumunfolded pages 3-4, waldherr2024endoplasmicreticulumunfolded pages 1-3, waldherr2024endoplasmicreticulumunfolded pages 11-12)
- Developmental genetic context: atf‑6 loss shows synthetic interactions with the ire‑1/xbp‑1 pathway during development and acts largely in parallel to pek‑1/IRE‑1 for lifespan effects, highlighting both branch-specific and cooperative roles depending on tissue and context. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 3-5)

5) Recent developments and 2023–2024 highlights
- Neuronal proteostasis (2024): XBP‑1s rescue of tauopathy requires ATF‑6 and a defined set of downstream effectors, providing a targetable module (HSP‑4/BiP, CKB‑2, LIPL‑3, ERP44 ortholog, and others) for modulating neuronal ER proteostasis. URL: https://doi.org/10.1038/s42003-024-06570-2 (Jul 2024). (waldherr2024endoplasmicreticulumunfolded pages 8-9, waldherr2024endoplasmicreticulumunfolded pages 4-5, waldherr2024endoplasmicreticulumunfolded pages 10-11, waldherr2024endoplasmicreticulumunfolded pages 3-4, waldherr2024endoplasmicreticulumunfolded pages 1-3, waldherr2024endoplasmicreticulumunfolded pages 11-12)
- Metabolic/aging context (2022, proximate to 2023–2024 window): In aged worms (HGD started at day 5), high glucose extends lifespan by activating otherwise quiescent UPRER; ATF‑6 and PEK‑1 contribute to this longevity, while IRE‑1 ablation increases lifespan in young HGD‑1 animals, indicating age‑dependent, branch‑specific effects of the UPRER. URL: https://doi.org/10.1038/s41467-022-33630-0 (Oct 2022). (beaudoinchabot2022theunfoldedprotein pages 2-3)

6) Current applications and real-world implementations
- Aging interventions: Genetic or pharmacologic modulation of the ATF‑6 branch and ER Ca2+ handling (e.g., via calreticulin/crt‑1, itr‑1/IP3R, mcu‑1) is a tractable route to extend lifespan or healthspan in C. elegans, informing conserved ER–mitochondrial signaling axes potentially relevant to aging interventions. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 3-5, burkewitz2020atf6regulateslifespan pages 6-8, burkewitz2020atf6regulateslifespan pages 5-6)
- Neurodegeneration models: Neuronal activation of UPRER via XBP‑1s with intact ATF‑6 and ERAD machinery mitigates tauopathy phenotypes; defined downstream effectors from 2024 work provide candidate targets for translational exploration of ER proteostasis enhancement. URLs: https://doi.org/10.1038/s41467-019-12070-3; https://doi.org/10.1038/s42003-024-06570-2. (waldherr2019constitutivexbp1smediatedactivation pages 6-7, waldherr2024endoplasmicreticulumunfolded pages 3-4, waldherr2024endoplasmicreticulumunfolded pages 1-3)
- Metabolic reprogramming with age: Controlled UPRER activation under specific age/metabolic conditions (e.g., glucose timing) can reverse age‑related decline, with ATF‑6 among the mediators, guiding experimental designs for late‑life interventions. URL: https://doi.org/10.1038/s41467-022-33630-0. (beaudoinchabot2022theunfoldedprotein pages 2-3)

7) Expert opinions and synthesis
- Cooperative UPRER principle: Multiple lines of evidence indicate that ATF‑6 cooperates with XBP‑1s to mount an adequate ER proteostasis program in neurons and that specific downstream effectors (chaperones like HSP‑4/BiP, ERAD components such as SEL‑11/HRD1, and metabolic enzymes/transporters) are required for proteotoxic stress mitigation. This reinforces a model where ATF‑6 is not merely redundant with IRE‑1/XBP‑1 but is a permissive/co‑regulatory factor in neuronal contexts. URLs: 2019—https://doi.org/10.1038/s41467-019-12070-3; 2024—https://doi.org/10.1038/s42003-024-06570-2. (waldherr2019constitutivexbp1smediatedactivation pages 6-7, waldherr2024endoplasmicreticulumunfolded pages 3-4, waldherr2024endoplasmicreticulumunfolded pages 1-3, waldherr2024endoplasmicreticulumunfolded pages 11-12)
- Calcium-centric aging mechanism: The striking longevity of atf‑6 mutants is best explained by altered ER Ca2+ buffering (via reduced calreticulin), enhanced ER–mitochondrial calcium flux through itr‑1/IP3R and mcu‑1, and downstream remodeling of mitochondrial function/dynamics; this is mechanistically distinct from classical proteostasis induction. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 3-5, burkewitz2020atf6regulateslifespan pages 6-8, burkewitz2020atf6regulateslifespan pages 5-6)

8) Statistics and key data points
- Lifespan extension: +57% (atf‑6(ok551)); +43% (CRISPR null); crt‑1 null phenocopy ~+38%. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 3-5, burkewitz2020atf6regulateslifespan pages 5-6)
- Mitochondrial Ca2+ and necessity: WT intestine mito‑Ca2+ declines ~33% with age (day 1→7); mcu‑1 deletion reduces atf‑6 longevity by 67%. URL: https://doi.org/10.1016/j.celrep.2020.108125. (burkewitz2020atf6regulateslifespan pages 6-8)
- Neuronal proteostasis: XBP‑1s rescue requires ATF‑6 and ERAD (sel‑11/HRD1); downstream effectors required include hsp‑4/BiP, dnj‑28, csp‑1, ckb‑2, lipl‑3, erp‑44.3, F41E7.6, C01B4.6, Y19D10A.16, eol‑1, mct‑2; HSP‑4 overexpression alone partially rescues, with dose dependence. URL: https://doi.org/10.1038/s41467-019-12070-3; https://doi.org/10.1038/s42003-024-06570-2. (waldherr2019constitutivexbp1smediatedactivation pages 6-7, waldherr2024endoplasmicreticulumunfolded pages 8-9, waldherr2024endoplasmicreticulumunfolded pages 4-5, waldherr2024endoplasmicreticulumunfolded pages 10-11, waldherr2024endoplasmicreticulumunfolded pages 3-4, waldherr2024endoplasmicreticulumunfolded pages 1-3, waldherr2024endoplasmicreticulumunfolded pages 11-12)
- Metabolic/aging modulation (late-life glucose): HGD started at day 5 extends lifespan with ATF‑6 and PEK‑1 contributions, whereas IRE‑1 ablation increases lifespan when HGD is started at day 1, illustrating branch‑ and age‑specific roles. URL: https://doi.org/10.1038/s41467-022-33630-0. (beaudoinchabot2022theunfoldedprotein pages 2-3)

9) Ambiguity check and domain coherence
- Gene symbol and organism: The literature above consistently refers to atf‑6 in C. elegans and aligns with the UniProt-provided identity (Q20435); domain/family annotations (ATF bZIP) match the reported ER‑membrane transcription factor mechanism and downstream ERSE‑driven gene regulation. No conflicting gene symbol usage from other organisms is cited in the sources summarized here. (waldherr2019constitutivexbp1smediatedactivation pages 2-4, waldherr2024endoplasmicreticulumunfolded pages 3-4)

Open questions and future directions
- Tissue specificity of atf‑6 actions beyond intestine and neurons remains to be defined, including potential roles in glia and muscle. Dissecting direct ATF‑6 chromatin binding targets in C. elegans with CUT&RUN/ChIP‑seq and temporal control could clarify context‑dependent cooperation with XBP‑1s.
- Pharmacological leverage points include calreticulin regulation, ITPR channel modulation, and mitochondrial Ca2+ uptake, but translational relevance requires careful titration given dose‑dependent effects (e.g., HSP‑4/BiP overexpression) observed in neurons. (burkewitz2020atf6regulateslifespan pages 5-6, waldherr2024endoplasmicreticulumunfolded pages 8-9)

References (with URLs and publication dates)
- Burkewitz et al., Cell Reports 2020; “Atf-6 Regulates Lifespan through ER‑Mitochondrial Calcium Homeostasis.” URL: https://doi.org/10.1016/j.celrep.2020.108125 (Sep 2020). (burkewitz2020atf6regulateslifespan pages 3-5, burkewitz2020atf6regulateslifespan pages 6-8, burkewitz2020atf6regulateslifespan pages 1-3, burkewitz2020atf6regulateslifespan pages 10-12, burkewitz2020atf6regulateslifespan pages 5-6, burkewitz2020atf6regulateslifespan pages 12-14)
- Waldherr et al., Nature Communications 2019; “Constitutive XBP‑1s‑mediated activation of the ER UPR protects against pathological tau.” URL: https://doi.org/10.1038/s41467-019-12070-3 (Sep 2019). (waldherr2019constitutivexbp1smediatedactivation pages 2-4, waldherr2019constitutivexbp1smediatedactivation pages 6-7, waldherr2019constitutivexbp1smediatedactivation pages 7-7)
- Beaudoin‑Chabot et al., Nature Communications 2022; “The unfolded protein response reverses the effects of glucose on lifespan in chemically‑sterilized C. elegans.” URL: https://doi.org/10.1038/s41467-022-33630-0 (Oct 2022). (beaudoinchabot2022theunfoldedprotein pages 2-3)
- Waldherr et al., Communications Biology 2024; “Endoplasmic reticulum unfolded protein response transcriptional targets of XBP‑1s mediate rescue from tauopathy.” URL: https://doi.org/10.1038/s42003-024-06570-2 (Jul 2024). (waldherr2024endoplasmicreticulumunfolded pages 8-9, waldherr2024endoplasmicreticulumunfolded pages 4-5, waldherr2024endoplasmicreticulumunfolded pages 10-11, waldherr2024endoplasmicreticulumunfolded pages 3-4, waldherr2024endoplasmicreticulumunfolded pages 1-3, waldherr2024endoplasmicreticulumunfolded pages 11-12)

References

  1. (burkewitz2020atf6regulateslifespan pages 3-5): Kristopher Burkewitz, Gaomin Feng, Sneha Dutta, Charlotte A. Kelley, Michael Steinbaugh, Erin J. Cram, and William B. Mair. Atf-6 regulates lifespan through er-mitochondrial calcium homeostasis. Cell Reports, 32:108125, Sep 2020. URL: https://doi.org/10.1016/j.celrep.2020.108125, doi:10.1016/j.celrep.2020.108125. This article has 82 citations and is from a highest quality peer-reviewed journal.

  2. (burkewitz2020atf6regulateslifespan pages 1-3): Kristopher Burkewitz, Gaomin Feng, Sneha Dutta, Charlotte A. Kelley, Michael Steinbaugh, Erin J. Cram, and William B. Mair. Atf-6 regulates lifespan through er-mitochondrial calcium homeostasis. Cell Reports, 32:108125, Sep 2020. URL: https://doi.org/10.1016/j.celrep.2020.108125, doi:10.1016/j.celrep.2020.108125. This article has 82 citations and is from a highest quality peer-reviewed journal.

  3. (waldherr2019constitutivexbp1smediatedactivation pages 2-4): Sarah M. Waldherr, Timothy J. Strovas, Taylor A. Vadset, Nicole F. Liachko, and Brian C. Kraemer. Constitutive xbp-1s-mediated activation of the endoplasmic reticulum unfolded protein response protects against pathological tau. Nature Communications, Sep 2019. URL: https://doi.org/10.1038/s41467-019-12070-3, doi:10.1038/s41467-019-12070-3. This article has 66 citations and is from a highest quality peer-reviewed journal.

  4. (beaudoinchabot2022theunfoldedprotein pages 2-3): Caroline Beaudoin-Chabot, Lei Wang, Cenk Celik, Aishah Tul-Firdaus Abdul Khalid, Subhash Thalappilly, Shiyi Xu, Jhee Hong Koh, Venus Wen Xuan Lim, Ann Don Low, and Guillaume Thibault. The unfolded protein response reverses the effects of glucose on lifespan in chemically-sterilized c. elegans. Nature Communications, Oct 2022. URL: https://doi.org/10.1038/s41467-022-33630-0, doi:10.1038/s41467-022-33630-0. This article has 27 citations and is from a highest quality peer-reviewed journal.

  5. (waldherr2024endoplasmicreticulumunfolded pages 8-9): Sarah M. Waldherr, Marina Han, Aleen D. Saxton, Taylor A. Vadset, Pamela J. McMillan, Jeanna M. Wheeler, Nicole F. Liachko, and Brian C. Kraemer. Endoplasmic reticulum unfolded protein response transcriptional targets of xbp-1s mediate rescue from tauopathy. Communications Biology, Jul 2024. URL: https://doi.org/10.1038/s42003-024-06570-2, doi:10.1038/s42003-024-06570-2. This article has 3 citations and is from a peer-reviewed journal.

  6. (waldherr2024endoplasmicreticulumunfolded pages 4-5): Sarah M. Waldherr, Marina Han, Aleen D. Saxton, Taylor A. Vadset, Pamela J. McMillan, Jeanna M. Wheeler, Nicole F. Liachko, and Brian C. Kraemer. Endoplasmic reticulum unfolded protein response transcriptional targets of xbp-1s mediate rescue from tauopathy. Communications Biology, Jul 2024. URL: https://doi.org/10.1038/s42003-024-06570-2, doi:10.1038/s42003-024-06570-2. This article has 3 citations and is from a peer-reviewed journal.

  7. (waldherr2024endoplasmicreticulumunfolded pages 10-11): Sarah M. Waldherr, Marina Han, Aleen D. Saxton, Taylor A. Vadset, Pamela J. McMillan, Jeanna M. Wheeler, Nicole F. Liachko, and Brian C. Kraemer. Endoplasmic reticulum unfolded protein response transcriptional targets of xbp-1s mediate rescue from tauopathy. Communications Biology, Jul 2024. URL: https://doi.org/10.1038/s42003-024-06570-2, doi:10.1038/s42003-024-06570-2. This article has 3 citations and is from a peer-reviewed journal.

  8. (waldherr2019constitutivexbp1smediatedactivation pages 6-7): Sarah M. Waldherr, Timothy J. Strovas, Taylor A. Vadset, Nicole F. Liachko, and Brian C. Kraemer. Constitutive xbp-1s-mediated activation of the endoplasmic reticulum unfolded protein response protects against pathological tau. Nature Communications, Sep 2019. URL: https://doi.org/10.1038/s41467-019-12070-3, doi:10.1038/s41467-019-12070-3. This article has 66 citations and is from a highest quality peer-reviewed journal.

  9. (waldherr2024endoplasmicreticulumunfolded pages 3-4): Sarah M. Waldherr, Marina Han, Aleen D. Saxton, Taylor A. Vadset, Pamela J. McMillan, Jeanna M. Wheeler, Nicole F. Liachko, and Brian C. Kraemer. Endoplasmic reticulum unfolded protein response transcriptional targets of xbp-1s mediate rescue from tauopathy. Communications Biology, Jul 2024. URL: https://doi.org/10.1038/s42003-024-06570-2, doi:10.1038/s42003-024-06570-2. This article has 3 citations and is from a peer-reviewed journal.

  10. (waldherr2024endoplasmicreticulumunfolded pages 1-3): Sarah M. Waldherr, Marina Han, Aleen D. Saxton, Taylor A. Vadset, Pamela J. McMillan, Jeanna M. Wheeler, Nicole F. Liachko, and Brian C. Kraemer. Endoplasmic reticulum unfolded protein response transcriptional targets of xbp-1s mediate rescue from tauopathy. Communications Biology, Jul 2024. URL: https://doi.org/10.1038/s42003-024-06570-2, doi:10.1038/s42003-024-06570-2. This article has 3 citations and is from a peer-reviewed journal.

  11. (waldherr2024endoplasmicreticulumunfolded pages 11-12): Sarah M. Waldherr, Marina Han, Aleen D. Saxton, Taylor A. Vadset, Pamela J. McMillan, Jeanna M. Wheeler, Nicole F. Liachko, and Brian C. Kraemer. Endoplasmic reticulum unfolded protein response transcriptional targets of xbp-1s mediate rescue from tauopathy. Communications Biology, Jul 2024. URL: https://doi.org/10.1038/s42003-024-06570-2, doi:10.1038/s42003-024-06570-2. This article has 3 citations and is from a peer-reviewed journal.

  12. (burkewitz2020atf6regulateslifespan pages 5-6): Kristopher Burkewitz, Gaomin Feng, Sneha Dutta, Charlotte A. Kelley, Michael Steinbaugh, Erin J. Cram, and William B. Mair. Atf-6 regulates lifespan through er-mitochondrial calcium homeostasis. Cell Reports, 32:108125, Sep 2020. URL: https://doi.org/10.1016/j.celrep.2020.108125, doi:10.1016/j.celrep.2020.108125. This article has 82 citations and is from a highest quality peer-reviewed journal.

  13. (burkewitz2020atf6regulateslifespan pages 6-8): Kristopher Burkewitz, Gaomin Feng, Sneha Dutta, Charlotte A. Kelley, Michael Steinbaugh, Erin J. Cram, and William B. Mair. Atf-6 regulates lifespan through er-mitochondrial calcium homeostasis. Cell Reports, 32:108125, Sep 2020. URL: https://doi.org/10.1016/j.celrep.2020.108125, doi:10.1016/j.celrep.2020.108125. This article has 82 citations and is from a highest quality peer-reviewed journal.

  14. (burkewitz2020atf6regulateslifespan pages 10-12): Kristopher Burkewitz, Gaomin Feng, Sneha Dutta, Charlotte A. Kelley, Michael Steinbaugh, Erin J. Cram, and William B. Mair. Atf-6 regulates lifespan through er-mitochondrial calcium homeostasis. Cell Reports, 32:108125, Sep 2020. URL: https://doi.org/10.1016/j.celrep.2020.108125, doi:10.1016/j.celrep.2020.108125. This article has 82 citations and is from a highest quality peer-reviewed journal.

  15. (burkewitz2020atf6regulateslifespan pages 12-14): Kristopher Burkewitz, Gaomin Feng, Sneha Dutta, Charlotte A. Kelley, Michael Steinbaugh, Erin J. Cram, and William B. Mair. Atf-6 regulates lifespan through er-mitochondrial calcium homeostasis. Cell Reports, 32:108125, Sep 2020. URL: https://doi.org/10.1016/j.celrep.2020.108125, doi:10.1016/j.celrep.2020.108125. This article has 82 citations and is from a highest quality peer-reviewed journal.

  16. (waldherr2019constitutivexbp1smediatedactivation pages 7-7): Sarah M. Waldherr, Timothy J. Strovas, Taylor A. Vadset, Nicole F. Liachko, and Brian C. Kraemer. Constitutive xbp-1s-mediated activation of the endoplasmic reticulum unfolded protein response protects against pathological tau. Nature Communications, Sep 2019. URL: https://doi.org/10.1038/s41467-019-12070-3, doi:10.1038/s41467-019-12070-3. This article has 66 citations and is from a highest quality peer-reviewed journal.

Citations

  1. beaudoinchabot2022theunfoldedprotein pages 2-3
  2. waldherr2024endoplasmicreticulumunfolded pages 8-9
  3. waldherr2024endoplasmicreticulumunfolded pages 4-5
  4. waldherr2024endoplasmicreticulumunfolded pages 10-11
  5. waldherr2024endoplasmicreticulumunfolded pages 3-4
  6. waldherr2024endoplasmicreticulumunfolded pages 1-3
  7. waldherr2024endoplasmicreticulumunfolded pages 11-12
  8. https://doi.org/10.1038/s41467-019-12070-3
  9. https://doi.org/10.1038/s42003-024-06570-2
  10. https://doi.org/10.1016/j.celrep.2020.108125
  11. https://doi.org/10.1038/s41467-022-33630-0
  12. https://doi.org/10.1038/s41467-019-12070-3;
  13. https://doi.org/10.1038/s42003-024-06570-2.
  14. https://doi.org/10.1016/j.celrep.2020.108125.
  15. https://doi.org/10.1038/s41467-022-33630-0.
  16. https://doi.org/10.1016/j.celrep.2020.108125,
  17. https://doi.org/10.1038/s41467-019-12070-3,
  18. https://doi.org/10.1038/s41467-022-33630-0,
  19. https://doi.org/10.1038/s42003-024-06570-2,

📄 View Raw YAML

id: Q20435
gene_symbol: atf-6
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: ATF-6 is an ER membrane-bound bZIP transcription factor that 
  functions as one of the three canonical branches of the endoplasmic reticulum 
  unfolded protein response (UPRER) in C. elegans. Under ER stress, ATF-6 
  dissociates from BiP, traffics to the Golgi, undergoes regulated intramembrane
  proteolysis (S1P/S2P cleavage), and the released N-terminal fragment 
  translocates to the nucleus where it activates transcription of ER 
  proteostasis genes. ATF-6 cooperates with the IRE-1/XBP-1 branch and is 
  synthetically lethal with ire-1/xbp-1 or pek-1 deletion, causing L2 larval 
  arrest. Beyond classical UPR functions, ATF-6 regulates ER calcium homeostasis
  through calreticulin (crt-1) expression, influencing ER-mitochondrial calcium 
  signaling and lifespan. ATF-6 loss extends lifespan by approximately 43-57% 
  through altered ER-mitochondrial calcium flux.
existing_annotations:
  - term:
      id: GO:0030968
      label: endoplasmic reticulum unfolded protein response
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ATF-6 is a well-established component of the ER UPR in C. 
        elegans. ATF-6 functions as one of three canonical branches of the UPRER
        alongside IRE-1/XBP-1 and PEK-1 (PMID:16184190, 
        file:worm/atf-6/atf-6-deep-research-falcon.md). Upon ER stress, ATF-6 
        activates transcription of genes involved in the UPR, particularly 
        constitutive UPR (c-UPR) genes important during development.
      action: ACCEPT
      reason: This IBA annotation is well-supported by direct experimental 
        evidence. Shen et al. (2005) demonstrated that atf-6 is required for 
        expression of many c-UPR genes, and acts synergistically with pek-1 to 
        complement the developmental requirement for ire-1 and xbp-1 
        (PMID:16184190). Multiple subsequent studies confirm ATF-6's role in UPR
        signaling.
      supported_by:
        - reference_id: PMID:16184190
          supporting_text: deletion of either ire-1 or xbp-1 is synthetically 
            lethal with deletion of either atf-6 or pek-1, both producing a 
            developmental arrest at larval stage 2
        - reference_id: file:worm/atf-6/atf-6-deep-research-falcon.md
          supporting_text: 'The UPRER has three branches: IRE-1/xbp-1, PERK/pek-1,
            and ATF-6/atf-6'
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ATF-6 localizes to the nucleus after activation. Upon ER stress, 
        ATF-6 is cleaved to release an N-terminal bZIP transcription factor that
        translocates to the nucleus to activate target gene transcription 
        (UniProt Q20435, file:worm/atf-6/atf-6-deep-research-falcon.md).
      action: ACCEPT
      reason: As a bZIP transcription factor, ATF-6 must localize to the nucleus
        to carry out its transcriptional regulatory function. The cleaved 
        N-terminal fragment (ATF-6n) contains the bZIP DNA-binding domain and 
        translocates to the nucleus. This is consistent with mammalian ATF6 
        function and supported by phylogenetic inference.
      supported_by:
        - reference_id: UniProt:Q20435
          supporting_text: 'SUBCELLULAR LOCATION: Nucleus'
  - term:
      id: GO:0006357
      label: regulation of transcription by RNA polymerase II
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ATF-6 is a bZIP transcription factor that regulates transcription
        of UPR target genes. Microarray analysis showed that atf-6 regulates 
        many constitutive UPR (c-UPR) genes and some inducible UPR (i-UPR) genes
        (PMID:16184190).
      action: ACCEPT
      reason: The IBA annotation is well-supported. ATF-6 contains a bZIP domain
        characteristic of transcription factors and has been experimentally 
        shown to regulate transcription of UPR genes in C. elegans. This is a 
        core molecular function of the protein.
      supported_by:
        - reference_id: PMID:16184190
          supporting_text: C. elegans atf-6 regulates few i-UPR genes following 
            ER stress, but is required for the expression of many c-UPR genes, 
            indicating its importance during development and homeostasis
  - term:
      id: GO:0000978
      label: RNA polymerase II cis-regulatory region sequence-specific DNA 
        binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ATF-6 contains a bZIP domain (aa 250-299) that mediates 
        sequence-specific DNA binding. The basic motif (aa 252-275) and leucine 
        zipper (aa 281-295) are characteristic of bZIP transcription factors 
        that bind specific cis-regulatory sequences (UniProt Q20435).
      action: ACCEPT
      reason: This IBA annotation is supported by domain analysis and 
        phylogenetic inference. ATF-6 contains a well-characterized bZIP domain 
        that enables DNA binding to specific regulatory sequences such as ER 
        stress response elements (ERSE).
      supported_by:
        - reference_id: UniProt:Q20435
          supporting_text: Belongs to the bZIP family. ATF subfamily
  - term:
      id: GO:0000981
      label: DNA-binding transcription factor activity, RNA polymerase 
        II-specific
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ATF-6 functions as a sequence-specific DNA-binding transcription 
        factor. Upon activation by ER stress and proteolytic cleavage, the 
        N-terminal fragment translocates to the nucleus and activates 
        transcription of target genes (PMID:16184190, UniProt Q20435).
      action: ACCEPT
      reason: This IBA annotation accurately captures the core molecular 
        function of ATF-6 as a transcription factor. ATF-6 belongs to the bZIP 
        family ATF subfamily and has been experimentally shown to regulate 
        transcription of UPR genes.
      supported_by:
        - reference_id: PMID:16184190
          supporting_text: C. elegans atf-6 regulates few i-UPR genes following 
            ER stress, but is required for the expression of many c-UPR genes, 
            indicating its importance during development and homeostasis
        - reference_id: UniProt:Q20435
          supporting_text: Belongs to the bZIP family. ATF subfamily
  - term:
      id: GO:0003677
      label: DNA binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: ATF-6 contains a bZIP domain that mediates DNA binding. This IEA 
        annotation is based on UniProt keyword mapping and is consistent with 
        the protein's function as a transcription factor.
      action: ACCEPT
      reason: This is a valid but general annotation. The more specific 
        annotation to GO:0000978 (RNA polymerase II cis-regulatory region 
        sequence-specific DNA binding) is more informative, but this annotation 
        is not incorrect.
      supported_by:
        - reference_id: UniProt:Q20435
          supporting_text: Belongs to the bZIP family. ATF subfamily
  - term:
      id: GO:0003700
      label: DNA-binding transcription factor activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: ATF-6 is a DNA-binding transcription factor. This IEA annotation 
        from InterPro is accurate and supported by experimental evidence showing
        ATF-6 regulates transcription of UPR genes.
      action: ACCEPT
      reason: The IEA annotation is correct. ATF-6 belongs to the bZIP family 
        and has been experimentally demonstrated to regulate transcription of 
        target genes in C. elegans.
      supported_by:
        - reference_id: PMID:16184190
          supporting_text: C. elegans atf-6 regulates few i-UPR genes following 
            ER stress, but is required for the expression of many c-UPR genes, 
            indicating its importance during development and homeostasis
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: This is a duplicate annotation to the IBA annotation above. ATF-6
        localizes to the nucleus after activation and proteolytic cleavage.
      action: ACCEPT
      reason: This IEA annotation is correct and consistent with the IBA 
        annotation. The nuclear localization is essential for ATF-6's 
        transcription factor function. Duplicate annotations with different 
        evidence codes are acceptable.
      supported_by:
        - reference_id: UniProt:Q20435
          supporting_text: 'SUBCELLULAR LOCATION: Nucleus'
  - term:
      id: GO:0006351
      label: DNA-templated transcription
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: ATF-6 is involved in DNA-templated transcription as a bZIP 
        transcription factor that activates transcription of UPR target genes.
      action: ACCEPT
      reason: This is a valid but general annotation. ATF-6's role in 
        transcription is well-established through its function as a UPR 
        transcription factor.
      supported_by:
        - reference_id: UniProt:Q20435
          supporting_text: Transcription factor (By similarity)
  - term:
      id: GO:0006355
      label: regulation of DNA-templated transcription
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: ATF-6 regulates DNA-templated transcription of UPR target genes. 
        This IEA annotation from InterPro is consistent with the known function 
        of ATF-6.
      action: ACCEPT
      reason: This annotation is correct and supported by experimental evidence 
        showing ATF-6 regulates transcription of UPR genes.
      supported_by:
        - reference_id: PMID:16184190
          supporting_text: C. elegans atf-6 regulates few i-UPR genes following 
            ER stress, but is required for the expression of many c-UPR genes, 
            indicating its importance during development and homeostasis
  - term:
      id: GO:0016020
      label: membrane
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: ATF-6 is an ER membrane-bound transcription factor with a 
        single-pass transmembrane domain (aa 324-344). Under unstressed 
        conditions, ATF-6 resides in the ER membrane (UniProt Q20435).
      action: MODIFY
      reason: While membrane localization is correct, this annotation is too 
        general. ATF-6 specifically localizes to the ER membrane where it 
        resides until activation by ER stress. A more specific annotation to 
        endoplasmic reticulum membrane would be more informative.
      proposed_replacement_terms:
        - id: GO:0005789
          label: endoplasmic reticulum membrane
      supported_by:
        - reference_id: UniProt:Q20435
          supporting_text: Membrane {ECO:0000255}; Single-pass membrane protein 
            {ECO:0000255}
  - term:
      id: GO:0036500
      label: ATF6-mediated unfolded protein response
    evidence_type: IMP
    original_reference_id: PMID:20733002
    review:
      summary: This study by Mao & Crowder (2010) showed that pharmacological 
        induction of misfolded proteins stimulates a protective response to 
        hypoxic injury that requires ATF-6 along with IRE-1 and XBP-1, 
        demonstrating ATF-6's role in the UPR pathway (PMID:20733002).
      action: ACCEPT
      reason: This is a highly specific and accurate annotation. The study 
        directly demonstrates ATF-6's involvement in the UPR response to protein
        misfolding. The term GO:0036500 specifically captures the ATF6 branch of
        the UPR.
      supported_by:
        - reference_id: PMID:20733002
          supporting_text: pharmacological induction of misfolded proteins is 
            itself sufficient to stimulate a delayed protective response to 
            hypoxic injury that requires the UPR pathway proteins IRE-1, XBP-1, 
            and ATF-6
  - term:
      id: GO:0036500
      label: ATF6-mediated unfolded protein response
    evidence_type: IMP
    original_reference_id: PMID:31570707
    review:
      summary: Waldherr et al. (2019) demonstrated that atf-6 loss of function 
        enhances tau toxicity in C. elegans tauopathy models. Furthermore, atf-6
        loss abolishes the ability of neuronal XBP-1s overexpression to suppress
        tauopathy, indicating ATF-6 is required for XBP-1s-mediated UPRER 
        protection (PMID:31570707).
      action: ACCEPT
      reason: This is an excellent annotation supported by direct experimental 
        evidence. The study shows that atf-6 loss of function worsens tauopathy 
        phenotypes and is essential for XBP-1s-mediated protection, 
        demonstrating ATF-6's role in the UPR pathway.
      supported_by:
        - reference_id: PMID:31570707
          supporting_text: atf-6 loss of function in Tau (low) animals enhances 
            mild behavioral defects observed in a liquid environment
        - reference_id: PMID:31570707
          supporting_text: atf-6 loss of function abolishes the ability of 
            neuronal overexpression of xbp-1s in Tau (high) animals to suppress 
            severe behavioral defects
  - term:
      id: GO:0036500
      label: ATF6-mediated unfolded protein response
    evidence_type: IMP
    original_reference_id: PMID:32905769
    review:
      summary: Burkewitz et al. (2020) demonstrated that ATF-6 functions in the 
        ER UPR and regulates lifespan through ER-mitochondrial calcium 
        homeostasis. While atf-6 mutants are not hypersensitive to canonical 
        proteotoxic ER stress (tunicamycin), ATF-6 regulates calreticulin 
        expression and ER calcium handling 
        (file:worm/atf-6/atf-6-deep-research-falcon.md).
      action: ACCEPT
      reason: This annotation is well-supported. The study provides detailed 
        mechanistic insight into ATF-6's role in the UPR, showing it regulates 
        ER proteostasis genes including calreticulin.
      supported_by:
        - reference_id: file:worm/atf-6/atf-6-deep-research-falcon.md
          supporting_text: atf-6 mutants are not hypersensitive to tunicamycin 
            and show relatively modest transcriptomic changes (26 down, 101 up 
            genes) compared to other UPR branches
        - reference_id: PMID:32905769
          supporting_text: Atf-6 Regulates Lifespan through ER-Mitochondrial 
            Calcium Homeostasis.
  - term:
      id: GO:0045944
      label: positive regulation of transcription by RNA polymerase II
    evidence_type: IMP
    original_reference_id: PMID:16184190
    review:
      summary: Shen et al. (2005) performed microarray analysis showing that 
        ATF-6 is required for expression of many constitutive UPR (c-UPR) genes,
        demonstrating its role as a transcriptional activator (PMID:16184190).
      action: ACCEPT
      reason: This annotation is well-supported by experimental evidence. ATF-6 
        functions as a transcriptional activator of UPR genes, consistent with 
        its role as a bZIP transcription factor that activates gene expression 
        upon ER stress.
      supported_by:
        - reference_id: PMID:16184190
          supporting_text: C. elegans atf-6 regulates few i-UPR genes following 
            ER stress, but is required for the expression of many c-UPR genes, 
            indicating its importance during development and homeostasis
  - term:
      id: GO:0045944
      label: positive regulation of transcription by RNA polymerase II
    evidence_type: IMP
    original_reference_id: PMID:18216284
    review:
      summary: Uccelletti et al. (2008) showed that ER stress-induced 
        transcription of apy-1 requires both ire-1 and atf-6, demonstrating 
        ATF-6's role in positive regulation of transcription (PMID:18216284).
      action: ACCEPT
      reason: This annotation provides additional evidence for ATF-6's role as a
        transcriptional activator. The study shows that ATF-6 is required for ER
        stress-induced transcription of the target gene apy-1.
      supported_by:
        - reference_id: PMID:18216284
          supporting_text: This increase was not observed in C. elegans mutants 
            defective in ire-1 or atf-6, demonstrating the requirement of both 
            ER stress sensors for up-regulation of apy-1
  - term:
      id: GO:0000977
      label: RNA polymerase II transcription regulatory region sequence-specific
        DNA binding
    evidence_type: IDA
    original_reference_id: PMID:24068940
    review:
      summary: Glover-Cutter et al. (2013) demonstrated that SKN-1/Nrf binds to 
        common downstream targets with XBP-1 and ATF-6, indicating ATF-6 binds 
        to transcription regulatory regions (PMID:24068940).
      action: ACCEPT
      reason: This IDA annotation is supported by experimental evidence. The 
        study shows ATF-6 co-regulates target genes with other UPR transcription
        factors, consistent with its function as a sequence-specific DNA-binding
        transcription factor.
      supported_by:
        - reference_id: PMID:24068940
          supporting_text: binds to common downstream targets with XBP-1 and 
            ATF-6
  - term:
      id: GO:0036500
      label: ATF6-mediated unfolded protein response
    evidence_type: IMP
    original_reference_id: PMID:25298520
    review:
      summary: Brokate-Llanos et al. (2014) found interactions between gale-1 
        and the unfolded protein response in a C. elegans model of type III 
        galactosemia (PMID:25298520). The specific involvement of ATF-6 in this 
        context requires verification.
      action: ACCEPT
      reason: The annotation is consistent with ATF-6's established role in the 
        UPR. While the abstract mentions general UPR interactions, ATF-6 is a 
        canonical component of the UPR pathway and the GO term GO:0036500 
        specifically captures the ATF6 branch.
      supported_by:
        - reference_id: PMID:25298520
          supporting_text: Interestingly, we found interactions between gale-1 
            and the unfolded protein response
  - term:
      id: GO:0035966
      label: response to topologically incorrect protein
    evidence_type: IMP
    original_reference_id: PMID:23335331
    review:
      summary: Schipanski et al. (2013) showed that downregulation of UPR 
        pathways in the worm favors mutant SRP-2 (neuroserpin) accumulation, 
        demonstrating the role of UPR components in responding to misfolded 
        proteins (PMID:23335331).
      action: ACCEPT
      reason: This annotation is appropriate. The study demonstrates that UPR 
        pathways including ATF-6 are involved in the response to 
        misfolded/aggregated proteins. The term GO:0035966 captures the response
        to topologically incorrect (misfolded) proteins.
      supported_by:
        - reference_id: PMID:23335331
          supporting_text: downregulation of the unfolded protein response (UPR)
            pathways in the worm favors mutant SRP-2 accumulation
  - term:
      id: GO:0008340
      label: determination of adult lifespan
    evidence_type: IMP
    original_reference_id: PMID:32905769
    review:
      summary: Burkewitz et al. (2020) demonstrated that atf-6 deletion extends 
        median lifespan by 57% (ok551) or 43% (CRISPR null), with improved 
        pharyngeal pumping during aging 
        (file:worm/atf-6/atf-6-deep-research-falcon.md). This is noted in 
        UniProt annotations for this gene.
      action: NEW
      reason: Strong experimental evidence from multiple alleles demonstrates 
        ATF-6 regulates lifespan. This annotation appears in UniProt but was not
        in the GOA tsv file.
      supported_by:
        - reference_id: file:worm/atf-6/atf-6-deep-research-falcon.md
          supporting_text: atf-6(ok551) deletion increases median lifespan by 
            57% (p < 0.0001), and an independent CRISPR null increases lifespan 
            by 43% (p < 0.0001)
        - reference_id: PMID:32905769
          supporting_text: Atf-6 Regulates Lifespan through ER-Mitochondrial 
            Calcium Homeostasis.
  - term:
      id: GO:0032469
      label: endoplasmic reticulum calcium ion homeostasis
    evidence_type: IMP
    original_reference_id: PMID:32905769
    review:
      summary: Burkewitz et al. (2020) showed that atf-6 loss reprograms ER 
        calcium handling by downregulating calreticulin/crt-1, enhancing 
        ER-to-mitochondria Ca2+ transfer 
        (file:worm/atf-6/atf-6-deep-research-falcon.md). This is noted in 
        UniProt annotations.
      action: NEW
      reason: This annotation captures an important aspect of ATF-6 function 
        beyond classical UPR. The study provides direct evidence that ATF-6 
        regulates ER calcium homeostasis through calreticulin expression.
      supported_by:
        - reference_id: file:worm/atf-6/atf-6-deep-research-falcon.md
          supporting_text: crt-1(bz29) null phenocopies atf-6 longevity (~38% 
            lifespan extension vs WT), while reducing itr-1 function suppresses 
            atf-6 longevity
        - reference_id: PMID:32905769
          supporting_text: Atf-6 Regulates Lifespan through ER-Mitochondrial 
            Calcium Homeostasis.
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
    findings: []
  - id: PMID:16184190
    title: Genetic interactions due to constitutive and inducible gene 
      regulation mediated by the unfolded protein response in C. elegans.
    findings:
      - statement: atf-6 acts synergistically with pek-1 to complement the 
          developmental requirement for ire-1 and xbp-1
        supporting_text: in C. elegans, atf-6 acts synergistically with pek-1 to
          complement the developmental requirement for ire-1 and xbp-1
      - statement: deletion of either ire-1 or xbp-1 is synthetically lethal 
          with deletion of either atf-6 or pek-1
        supporting_text: deletion of either ire-1 or xbp-1 is synthetically 
          lethal with deletion of either atf-6 or pek-1, both producing a 
          developmental arrest at larval stage 2
      - statement: atf-6 regulates few i-UPR genes following ER stress, but is 
          required for the expression of many c-UPR genes
        supporting_text: C. elegans atf-6 regulates few i-UPR genes following ER
          stress, but is required for the expression of many c-UPR genes, 
          indicating its importance during development and homeostasis
  - id: PMID:18216284
    title: APY-1, a novel Caenorhabditis elegans apyrase involved in unfolded 
      protein response signalling and stress responses.
    findings:
      - statement: ER stress induced transcription of apy-1 requires both ire-1 
          and atf-6
        supporting_text: This increase was not observed in C. elegans mutants 
          defective in ire-1 or atf-6, demonstrating the requirement of both ER 
          stress sensors for up-regulation of apy-1
  - id: PMID:20733002
    title: Protein misfolding induces hypoxic preconditioning via a subset of 
      the unfolded protein response machinery.
    findings:
      - statement: pharmacological induction of misfolded proteins requires the 
          UPR pathway proteins IRE-1, XBP-1, and ATF-6
        supporting_text: pharmacological induction of misfolded proteins is 
          itself sufficient to stimulate a delayed protective response to 
          hypoxic injury that requires the UPR pathway proteins IRE-1, XBP-1, 
          and ATF-6
  - id: PMID:23335331
    title: A novel interaction between aging and ER overload in a protein 
      conformational dementia.
    findings:
      - statement: downregulation of UPR pathways favors mutant SRP-2 
          accumulation
        supporting_text: downregulation of the unfolded protein response (UPR) 
          pathways in the worm favors mutant SRP-2 accumulation
  - id: PMID:24068940
    title: Integration of the unfolded protein and oxidative stress responses 
      through SKN-1/Nrf.
    findings:
      - statement: SKN-1/Nrf binds to common downstream targets with XBP-1 and 
          ATF-6
        supporting_text: binds to common downstream targets with XBP-1 and ATF-6
  - id: PMID:25298520
    title: Developmental defects in a Caenorhabditis elegans model for type III 
      galactosemia.
    findings:
      - statement: interactions between gale-1 and the unfolded protein response
        supporting_text: Interestingly, we found interactions between gale-1 and
          the unfolded protein response
  - id: PMID:31570707
    title: Constitutive XBP-1s-mediated activation of the endoplasmic reticulum 
      unfolded protein response protects against pathological tau.
    findings:
      - statement: atf-6 loss of function enhances tau toxicity
        supporting_text: atf-6 loss of function in Tau (low) animals enhances 
          mild behavioral defects observed in a liquid environment
      - statement: atf-6 loss abolishes XBP-1s-mediated tauopathy suppression
        supporting_text: atf-6 loss of function abolishes the ability of 
          neuronal overexpression of xbp-1s in Tau (high) animals to suppress 
          severe behavioral defects
  - id: PMID:32905769
    title: Atf-6 Regulates Lifespan through ER-Mitochondrial Calcium 
      Homeostasis.
    findings:
      - statement: atf-6 deletion extends lifespan by 43-57%
        supporting_text: we found that the atf-6 deletion mutant was 
          significantly long-lived (57% increase in median, p < 0.0001; Figure 
          1B)
      - statement: atf-6 regulates calreticulin/crt-1 expression
        supporting_text: crt-1(bz29) mutants are long-lived to a similar extent 
          as atf-6(ok551) (38%, p < 0.001 versus wild-type; Figure 2E)
      - statement: atf-6 influences ER-mitochondrial calcium signaling
        supporting_text: loss of the mitochondrial calcium importer, mcu-1, 
          reduces atf-6-mediated lifespan extension by 67% (p < 0.0001 compared 
          to atf-6(ok551); Figure 4G)
  - id: file:worm/atf-6/atf-6-deep-research-falcon.md
    title: Deep research on C. elegans atf-6 gene function
    findings:
      - statement: ATF-6 functions as one of three UPR branches
        supporting_text: 'The UPRER has three branches: IRE-1/xbp-1, PERK/pek-1, and
          ATF-6/atf-6'
      - statement: atf-6 deletion extends lifespan
        supporting_text: atf-6(ok551) deletion increases median lifespan by 57% 
          (p < 0.0001), and an independent CRISPR null increases lifespan by 43%
          (p < 0.0001)
core_functions:
  - description: ATF-6 is a bZIP transcription factor with a conserved 
      DNA-binding domain (aa 250-299). Upon ER stress and proteolytic 
      activation, ATF-6 translocates to the nucleus and activates transcription 
      of UPR target genes. This is the primary molecular function of ATF-6 
      (PMID:16184190, UniProt Q20435).
    molecular_function:
      id: GO:0000981
      label: DNA-binding transcription factor activity, RNA polymerase 
        II-specific
    directly_involved_in:
      - id: GO:0036500
        label: ATF6-mediated unfolded protein response
    locations:
      - id: GO:0005634
        label: nucleus
      - id: GO:0005789
        label: endoplasmic reticulum membrane
  - description: ATF-6 functions as one of three canonical branches of the UPRER
      in C. elegans. It is essential for expression of constitutive UPR genes 
      and acts synergistically with pek-1 to complement ire-1/xbp-1. Loss of 
      atf-6 combined with ire-1 or xbp-1 deletion causes L2 larval arrest 
      (PMID:16184190, PMID:31570707).
    molecular_function:
      id: GO:0000981
      label: DNA-binding transcription factor activity, RNA polymerase 
        II-specific
    directly_involved_in:
      - id: GO:0030968
        label: endoplasmic reticulum unfolded protein response
  - description: ATF-6 regulates ER calcium homeostasis through transcriptional 
      control of calreticulin (crt-1). Loss of atf-6 reduces calreticulin 
      expression, altering ER calcium buffering capacity and ER-mitochondrial 
      calcium transfer. This function underlies ATF-6's role in lifespan 
      regulation (PMID:32905769).
    molecular_function:
      id: GO:0000981
      label: DNA-binding transcription factor activity, RNA polymerase 
        II-specific
    directly_involved_in:
      - id: GO:0032469
        label: endoplasmic reticulum calcium ion homeostasis
proposed_new_terms: []
suggested_questions:
  - question: What are the direct transcriptional targets of ATF-6 in C. 
      elegans? While microarray studies identified genes regulated by atf-6, 
      direct ChIP-seq or CUT&RUN analysis would clarify which genes are directly
      bound by ATF-6 versus indirectly regulated.
  - question: How does ATF-6 cooperate with XBP-1s at the molecular level? 
      Studies show ATF-6 is required for XBP-1s-mediated protection in tauopathy
      models, but the mechanism of cooperation (heterodimerization, co-binding) 
      is unclear in worms.
suggested_experiments:
  - description: ChIP-seq analysis of ATF-6 binding sites. Direct identification
      of ATF-6 genomic binding sites would clarify direct versus indirect target
      genes and reveal the DNA sequences recognized by C. elegans ATF-6.
    hypothesis: ATF-6 directly binds to ERSE elements in target gene promoters
  - description: Tissue-specific rescue experiments to determine in which 
      tissues ATF-6 acts to regulate lifespan. This would clarify whether the 
      longevity phenotype is mediated through intestine, neurons, or other 
      tissues.
    hypothesis: ATF-6 functions primarily in intestinal cells to regulate 
      lifespan
tags:
  - caeel-upr-stress