atf-4

UniProt ID: Q22156
Organism: Caenorhabditis elegans
Review Status: COMPLETE
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Gene Description

ATF-4 (also known as ATF-5) is a bZIP transcription factor and the C. elegans ortholog of mammalian ATF4. It functions as a central effector of the integrated stress response (ISR), being preferentially translated when global protein synthesis is reduced due to eIF2alpha phosphorylation or other translation-suppressing conditions. ATF-4 contains two upstream open reading frames (uORFs) in its 5' UTR that normally suppress main-ORF translation; when ribosome initiation is slowed, these uORFs are bypassed, leading to increased ATF-4 protein synthesis. ATF-4 localizes to the nucleus and acts as a transcriptional activator, inducing expression of cytoprotective genes including heat shock proteins (sip-1, hsp-70, hsp-16.2) and the transsulfuration enzyme cth-2 (cystathionine gamma-lyase). The ATF-4/cth-2 axis increases hydrogen sulfide (H2S) production and protein persulfidation, which are protective modifications that contribute to longevity and stress resistance. ATF-4 overexpression extends lifespan by 7-44% and is required for longevity benefits from translation inhibition and mTORC1 suppression. ATF-4-driven longevity requires the canonical longevity transcription factors DAF-16/FOXO, HSF-1, and SKN-1/NRF.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding
IBA
GO_REF:0000033
ACCEPT
Summary: ATF-4 is a bZIP transcription factor that binds to DNA regulatory regions. The bZIP domain (residues 138-201) contains a basic motif (residues 140-163) for DNA binding and a leucine zipper (residues 173-187) for dimerization. Phylogenetic inference from ATF4 orthologs supports sequence-specific DNA binding activity. This is consistent with its function as a transcription factor that regulates target genes like cth-2 and heat shock proteins [PMID:35181679].
Reason: IBA annotation is well-supported by domain architecture (bZIP with basic DNA-binding motif) and functional evidence that ATF-4 directly regulates transcription of specific target genes including cth-2 and heat shock proteins.
Supporting Evidence:
PMID:35181679
ATF-4 overexpression upregulated several small heat shock protein (HSP) genes that are also controlled by HSF-1/HSF (heat shock factor) and DAF-16/FOXO
file:worm/atf-4/atf-4-deep-research-falcon.md
model: Edison Scientific Literature
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific
IBA
GO_REF:0000033
ACCEPT
Summary: ATF-4 functions as a transcriptional activator of cytoprotective and proteostasis genes. Overexpression of ATF-4 upregulates expression of target genes including cth-2 (cystathionine gamma-lyase), sip-1/CRYAA, hsp-70, hsp-16.2, and hsp-12.3 [PMID:35181679]. This demonstrates transcription activator function consistent with the phylogenetically-inferred annotation.
Reason: Strong experimental support from PMID:35181679 demonstrating ATF-4 positively regulates transcription of multiple target genes. IBA annotation is phylogenetically sound and consistent with characterized ATF4 function across species.
Supporting Evidence:
PMID:35181679
Each of the ATF-4-upregulated chaperone genes sip-1/CRYAA, hsp-70/HSPA1L, hsp-16.2/HSPB1, and hsp-12.3/HSPB2 was required for lifespan extension from ATF-4 overexpression
GO:0005634 nucleus
IBA
GO_REF:0000033
ACCEPT
Summary: Nuclear localization is supported by phylogenetic inference and is consistent with ATF-4's function as a transcription factor. The bZIP domain contains basic residues typical of nuclear localization. Direct experimental evidence is provided by IDA annotation from PMID:23692540 (see below).
Reason: IBA annotation is redundant with IDA evidence but correct. Nuclear localization is phylogenetically conserved and functionally required for transcription factor activity.
Supporting Evidence:
PMID:35181679
Transgenic ATF-4-overexpressing animals (ATF-4OE) exhibited nuclear accumulation of ATF-4 in neuronal, hypodermal, and other somatic tissues under unstressed conditions
GO:0006357 regulation of transcription by RNA polymerase II
IBA
GO_REF:0000033
ACCEPT
Summary: ATF-4 regulates RNA polymerase II-mediated transcription by binding to regulatory elements and activating expression of target genes. This is supported by experimental evidence showing ATF-4 overexpression increases transcription of target genes including cth-2, sip-1, and heat shock proteins [PMID:35181679].
Reason: Well-supported IBA annotation consistent with ATF-4's established role as a transcriptional regulator. The term appropriately captures the biological process without over-specifying.
Supporting Evidence:
PMID:35181679
ATF-4 overexpression upregulated several small heat shock protein (HSP) genes that are also controlled by HSF-1/HSF (heat shock factor) and DAF-16/FOXO
GO:0003677 DNA binding
IEA
GO_REF:0000043
ACCEPT
Summary: IEA annotation from UniProtKB keyword mapping. ATF-4 contains a bZIP domain (IPR004827) with a basic DNA-binding motif (residues 140-163). This general term is subsumed by the more specific IBA annotation for sequence-specific DNA binding (GO:0000977).
Reason: Correct but less specific than the IBA annotation for sequence-specific DNA binding. The annotation is valid as it captures the fundamental DNA-binding capability of the bZIP domain.
Supporting Evidence:
GO_REF:0000043
[Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping - DNA-binding keyword maps to GO:0003677]
GO:0003700 DNA-binding transcription factor activity
IEA
GO_REF:0000002
ACCEPT
Summary: IEA annotation from InterPro record association. ATF-4 contains the bZIP domain (IPR004827) which is associated with transcription factor activity. This is consistent with ATF-4's characterized function as a transcriptional activator.
Reason: Correct InterPro-based annotation. The bZIP domain definitively establishes ATF-4 as a DNA-binding transcription factor, and experimental evidence confirms this function.
Supporting Evidence:
GO_REF:0000002
[Gene Ontology annotation through association of InterPro records with GO terms - bZIP domain (IPR004827) associated with transcription factor activity]
GO:0005634 nucleus
IEA
GO_REF:0000044
ACCEPT
Summary: IEA annotation from UniProtKB subcellular location vocabulary mapping. Nuclear localization is also supported by IDA (PMID:23692540) and IBA evidence.
Reason: Correct annotation, redundant with IDA and IBA evidence. Nuclear localization is well-established.
Supporting Evidence:
GO_REF:0000044
[Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping]
GO:0006351 DNA-templated transcription
IEA
GO_REF:0000043
ACCEPT
Summary: IEA annotation from keyword mapping indicating involvement in transcription. ATF-4 participates in transcription as an activator, but this general term is less informative than the more specific GO:0006357 (regulation of transcription by RNA polymerase II).
Reason: Valid but general annotation. ATF-4 participates in DNA-templated transcription as a regulatory factor rather than as part of the core transcription machinery.
Supporting Evidence:
GO_REF:0000043
[Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping - Transcription keyword]
GO:0006355 regulation of DNA-templated transcription
IEA
GO_REF:0000002
ACCEPT
Summary: IEA annotation from InterPro association indicating transcriptional regulatory function. This is appropriately general and consistent with ATF-4's role as a transcription factor.
Reason: Correct annotation capturing ATF-4's regulatory role in transcription. Consistent with more specific annotations for RNA polymerase II transcription regulation.
Supporting Evidence:
GO_REF:0000002
[Gene Ontology annotation through association of InterPro records with GO terms - bZIP domain associated with transcription regulation]
GO:0045944 positive regulation of transcription by RNA polymerase II
IEA
GO_REF:0000108
ACCEPT
Summary: IEA annotation inferred from logical relationships. ATF-4 is established as a transcriptional activator based on the IBA annotation for GO:0001228 (DNA-binding transcription activator activity). Experimental evidence from PMID:35181679 confirms ATF-4 overexpression upregulates target gene expression.
Reason: Correct logical inference from transcription activator activity to positive regulation of transcription. Well-supported by experimental evidence demonstrating ATF-4 activates transcription of target genes.
Supporting Evidence:
PMID:35181679
ATF-4 overexpression upregulated several small heat shock protein (HSP) genes that are also controlled by HSF-1/HSF (heat shock factor) and DAF-16/FOXO
GO:0005515 protein binding
IPI
PMID:23661758
Networks of bZIP protein-protein interactions diversified ov...
MODIFY
Summary: This annotation derives from a large-scale study of bZIP protein-protein interactions across species, measuring 2891 protein pairs in vitro [PMID:23661758]. The study examined bZIP dimerization networks and found extensive rewiring of interactions. While the interaction data is valuable, the GO term "protein binding" is uninformative and should be replaced with a more specific term indicating bZIP dimerization.
Reason: The annotation captures real protein-protein interactions, but "protein binding" (GO:0005515) is too vague. ATF-4 dimerizes with other bZIP proteins through its leucine zipper domain. A more informative term would be "DNA-binding transcription factor binding" (GO:0140297) or annotation to a specific partner like CEBP-2 (documented in IntAct).
Supporting Evidence:
PMID:23661758
We studied the basic region-leucine zipper (bZIP) transcription factors and quantified bZIP dimerization networks for five metazoan and two single-cell species, measuring interactions in vitro for 2891 protein pairs
GO:0005515 protein binding
IPI
PMID:23791784
Extensive rewiring and complex evolutionary dynamics in a C....
MODIFY
Summary: This annotation is from a comprehensive study of C. elegans transcription factor networks that characterized interaction rewiring after gene duplication [PMID:23791784]. The study examined protein-protein and protein-DNA interactions across TF families. As with the other protein binding annotation, this term is too general.
Reason: Valid interaction data but "protein binding" is uninformative. The study examined TF networks, so more specific terms describing transcription factor complex formation or DNA-binding transcription factor binding would be more appropriate.
Supporting Evidence:
PMID:23791784
we comprehensively characterize such network rewiring for C. elegans transcription factors (TFs) within and across four newly delineated molecular networks
GO:0010628 positive regulation of gene expression
IMP
PMID:35181679
ATF-4 and hydrogen sulfide signalling mediate longevity in r...
ACCEPT
Summary: ATF-4 overexpression increases expression of multiple target genes including cth-2 (cystathionine gamma-lyase), sip-1/CRYAA, hsp-70, hsp-16.2, and hsp-12.3 as demonstrated by RNA-seq and qRT-PCR [PMID:35181679]. Loss of atf-4 reduces expression of these targets. This IMP annotation is well-supported by the experimental evidence.
Reason: Strong experimental evidence from overexpression and loss-of-function studies demonstrating ATF-4 positively regulates gene expression. The annotation accurately captures ATF-4's transcriptional activator function.
Supporting Evidence:
PMID:35181679
Each of the ATF-4-upregulated chaperone genes sip-1/CRYAA, hsp-70/HSPA1L, hsp-16.2/HSPB1, and hsp-12.3/HSPB2 was required for lifespan extension from ATF-4 overexpression
GO:0070814 hydrogen sulfide biosynthetic process
IMP
PMID:35181679
ATF-4 and hydrogen sulfide signalling mediate longevity in r...
ACCEPT
Summary: ATF-4 promotes hydrogen sulfide (H2S) biosynthesis by transcriptionally activating cth-2 (cystathionine gamma-lyase), which catalyzes H2S production in the transsulfuration pathway. ATF-4 overexpression increases H2S production capacity, while atf-4 loss reduces it. The H2S pathway is required for ATF-4-mediated longevity [PMID:35181679].
Reason: Strong experimental evidence demonstrating ATF-4 regulates H2S biosynthesis through transcriptional activation of cth-2. This is a key downstream effector pathway of ATF-4.
Supporting Evidence:
PMID:35181679
ATF-4 promotes longevity by activating canonical anti-ageing mechanisms, but also by elevating expression of the transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) production
GO:0005634 nucleus
IDA
PMID:23692540
The general control nonderepressible-2 kinase mediates stres...
ACCEPT
Summary: Direct experimental observation of ATF-4 (referred to as ATF-5 in this publication) localization to the nucleus. The study examined GCN-2 and its downstream targets in the context of TOR signaling and longevity. Nuclear localization is consistent with ATF-4's function as a transcription factor.
Reason: Primary experimental evidence (IDA) directly demonstrating nuclear localization. This is the strongest evidence code for this cellular component annotation.
Supporting Evidence:
PMID:35181679
Transgenic ATF-4-overexpressing animals (ATF-4OE) exhibited nuclear accumulation of ATF-4 in neuronal, hypodermal, and other somatic tissues under unstressed conditions
GO:0140467 integrated stress response signaling
IMP
PMID:35181679
ATF-4 and hydrogen sulfide signalling mediate longevity in r...
NEW
Summary: ATF-4 is a central effector of the integrated stress response (ISR). It is preferentially translated when eIF2alpha is phosphorylated or when global translation is suppressed. ATF-4 contains two uORFs in its 5' UTR that mediate this translational control. The ISR pathway converges on ATF-4 to activate cytoprotective gene programs [PMID:35181679].
Reason: This is a core function of ATF-4 that is not currently annotated. The deep research clearly establishes ATF-4 as a key ISR effector, and GO:0140467 specifically mentions ATF4 in its definition. This annotation should be added with IMP evidence.
Supporting Evidence:
PMID:35181679
ATF-4 is preferentially translated under conditions of reduced global protein synthesis
GO:0008340 determination of adult lifespan
IMP
PMID:35181679
ATF-4 and hydrogen sulfide signalling mediate longevity in r...
NEW
Summary: ATF-4 overexpression extends C. elegans lifespan by 7-44% across multiple independent trials and improves healthspan metrics. Loss of atf-4 abrogates longevity benefits from translation inhibition and mTORC1 suppression. ATF-4 is both necessary and sufficient for lifespan extension under specific conditions [PMID:35181679].
Reason: Lifespan regulation is a major characterized function of ATF-4 in C. elegans. The evidence is strong and direct (overexpression/loss-of-function lifespan assays). This core function should be annotated.
Supporting Evidence:
PMID:35181679
ATF-4 overexpression is sufficient to increase lifespan

Core Functions

ATF-4 is a bZIP transcription factor that activates expression of target genes including cth-2, sip-1, hsp-70, hsp-16.2, and hsp-12.3. Overexpression increases target gene expression; loss-of-function reduces it [PMID:35181679].

Supporting Evidence:
  • PMID:35181679
    Each of the ATF-4-upregulated chaperone genes sip-1/CRYAA, hsp-70/HSPA1L, hsp-16.2/HSPB1, and hsp-12.3/HSPB2 was required for lifespan extension from ATF-4 overexpression

ATF-4 promotes H2S biosynthesis by transcriptionally activating cth-2 (cystathionine gamma-lyase). The ATF-4/cth-2/H2S axis is required for longevity from mTORC1 inhibition and increases protective protein persulfidation [PMID:35181679].

Supporting Evidence:
  • PMID:35181679
    ATF-4 promotes longevity by activating canonical anti-ageing mechanisms, but also by elevating expression of the transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) production

References

Gene Ontology annotation through association of InterPro records with GO terms
  • ATF-4 bZIP domain (IPR004827) associated with transcription factor activity
Annotation inferences using phylogenetic trees
  • Phylogenetic inference from ATF4 orthologs supports DNA binding and transcription activator functions
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  • DNA-binding and Transcription keywords mapped to appropriate GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
  • Nucleus localization from UniProt subcellular location annotation
Automatic assignment of GO terms using logical inference, based on inter-ontology links
  • Positive regulation of transcription inferred from transcription activator activity
Networks of bZIP protein-protein interactions diversified over a billion years of evolution.
  • Comprehensive analysis of bZIP dimerization networks across species
    "We studied the basic region-leucine zipper (bZIP) transcription factors and quantified bZIP dimerization networks for five metazoan and two single-cell species, measuring interactions in vitro for 2891 protein pairs"
  • ATF-4 participates in heteromeric bZIP interactions
    "Metazoans have a higher proportion of heteromeric bZIP interactions and more network complexity than the single-cell species"
The general control nonderepressible-2 kinase mediates stress response and longevity induced by target of rapamycin inactivation in Caenorhabditis elegans.
  • GCN-2 kinase functions upstream of ATF-4 in stress response
  • ATF-4 (referred to as ATF-5) mediates longevity from TOR pathway inhibition
  • Nuclear localization of ATF-4 demonstrated
Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network.
  • Comprehensive characterization of C. elegans TF interaction networks
    "we comprehensively characterize such network rewiring for C. elegans transcription factors (TFs) within and across four newly delineated molecular networks"
  • ATF-4 participates in TF-TF interaction networks
    "Gene duplication results in two identical paralogs that diverge through mutation, leading to loss or gain of interactions with other biomolecules"
ATF-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mTORC1.
  • ATF-4 is preferentially translated under reduced protein synthesis conditions
    "ATF-4 is preferentially translated under conditions of reduced global protein synthesis"
  • ATF-4 contains two uORFs mediating translational control
    "The C. elegans atf-4 ortholog (previously named atf-5) contains two 5′ UTR uORFs"
  • ATF-4 overexpression extends lifespan 7-44%
    "ATF-4 overexpression increased lifespan by 7-44% across >10 independent trials"
  • ATF-4 activates cth-2 to increase H2S production
    "ATF-4 promotes longevity by activating canonical anti-ageing mechanisms, but also by elevating expression of the transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) production"
  • ATF-4 upregulates heat shock proteins (sip-1, hsp-70, hsp-16.2, hsp-12.3)
    "Each of the ATF-4-upregulated chaperone genes sip-1/CRYAA, hsp-70/HSPA1L, hsp-16.2/HSPB1, and hsp-12.3/HSPB2 was required for lifespan extension from ATF-4 overexpression"
  • ATF-4 localizes to nucleus in multiple somatic tissues
    "Transgenic ATF-4-overexpressing animals (ATF-4OE) exhibited nuclear accumulation of ATF-4 in neuronal, hypodermal, and other somatic tissues under unstressed conditions"
  • ATF-4-driven longevity requires DAF-16, HSF-1, and SKN-1
    "Each of those transcription factors is critical for lifespan extension arising from suppression of translation10,11, and we determined that they are also needed for longevity conferred by ATF-4 overexpression"
  • ATF-4 increases protein persulfidation through cth-2/H2S pathway
    "This H2S boost increases protein persulfidation, a protective modification of redox-reactive cysteines"
file:worm/atf-4/atf-4-deep-research-falcon.md
Deep research findings on atf-4 gene function
  • ATF-4 is a validated ATF4 ortholog that integrates translational and stress signals via uORF-mediated translational control

Suggested Questions for Experts

Q: What are the specific DNA binding sites/motifs recognized by C. elegans ATF-4? Are they canonical CRE (cAMP response element) sites or different from mammalian ATF4?

Suggested experts: T. Keith Blackwell, Collin Y. Ewald

Q: Does ATF-4 form heterodimers with specific bZIP partners in vivo, and do these partnerships affect target gene specificity?

Suggested experts: Amy E. Keating, Albertha J. Walhout

Q: What is the relative contribution of eIF2alpha-dependent vs. eIF2alpha-independent mechanisms to ATF-4 translation under different stress conditions?

Suggested experts: William B. Mair, Cole Haynes

Suggested Experiments

Experiment: ChIP-seq for ATF-4 to identify genome-wide binding sites and characterize the DNA motifs recognized by C. elegans ATF-4. This would definitively establish direct ATF-4 targets and allow comparison to mammalian ATF4 binding preferences.

Hypothesis: ATF-4 binds to canonical CRE or related motifs in promoters of target genes like cth-2 and heat shock proteins.

Type: ChIP-seq

Experiment: Tissue-specific rescue experiments to determine which tissues require ATF-4 for longevity (neuronal vs. intestinal vs. hypodermal). ATF-4 is expressed in multiple tissues; identifying the key tissue(s) for lifespan effects would inform the mechanism.

Hypothesis: ATF-4 acts in specific tissues (likely neurons or intestine) to coordinate organism-wide stress responses and longevity.

Type: Tissue-specific rescue

Tags

caeel-upr-stress

📚 Additional Documentation

Deep Research Falcon

(atf-4-deep-research-falcon.md)

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gene_id: atf-4
gene_symbol: atf-4
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protein_description: 'RecName: Full=Transcription factor atf-4 homolog {ECO:0000303|PubMed:35181679};
AltName: Full=cAMP-dependent transcription factor family member 4 {ECO:0000312|WormBase:T04C10.4};'
gene_info: Name=atf-4 {ECO:0000312|WormBase:T04C10.4}; Synonyms=atf-5 {ECO:0000312|WormBase:T04C10.4};
ORFNames=T04C10.4 {ECO:0000312|WormBase:T04C10.4};
organism_full: Caenorhabditis elegans.
protein_family: Belongs to the bZIP family. .
protein_domains: bZIP. (IPR004827); bZIP_sf. (IPR046347); bZIP_1 (PF00170)
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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: Q22156
  • Protein Description: RecName: Full=Transcription factor atf-4 homolog {ECO:0000303|PubMed:35181679}; AltName: Full=cAMP-dependent transcription factor family member 4 {ECO:0000312|WormBase:T04C10.4};
  • Gene Information: Name=atf-4 {ECO:0000312|WormBase:T04C10.4}; Synonyms=atf-5 {ECO:0000312|WormBase:T04C10.4}; ORFNames=T04C10.4 {ECO:0000312|WormBase:T04C10.4};
  • Organism (full): Caenorhabditis elegans.
  • Protein Family: Belongs to the bZIP family. .
  • Key Domains: bZIP. (IPR004827); bZIP_sf. (IPR046347); bZIP_1 (PF00170)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "atf-4" 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-4' 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-4 (gene ID: atf-4, UniProt: Q22156) 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: Q22156
  • Protein Description: RecName: Full=Transcription factor atf-4 homolog {ECO:0000303|PubMed:35181679}; AltName: Full=cAMP-dependent transcription factor family member 4 {ECO:0000312|WormBase:T04C10.4};
  • Gene Information: Name=atf-4 {ECO:0000312|WormBase:T04C10.4}; Synonyms=atf-5 {ECO:0000312|WormBase:T04C10.4}; ORFNames=T04C10.4 {ECO:0000312|WormBase:T04C10.4};
  • Organism (full): Caenorhabditis elegans.
  • Protein Family: Belongs to the bZIP family. .
  • Key Domains: bZIP. (IPR004827); bZIP_sf. (IPR046347); bZIP_1 (PF00170)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "atf-4" 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-4' 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-4 (gene ID: atf-4, UniProt: Q22156) 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.

Title: Functional annotation of C. elegans atf-4 (T04C10.4; UniProt Q22156)

Abstract
We review current knowledge on the Caenorhabditis elegans atf-4 gene product (UniProt Q22156), a basic leucine zipper (bZIP) transcription factor and ortholog of mammalian ATF4. We verify its identity and organismal context, summarize integrated stress response (ISR)-linked translational regulation via upstream open reading frames (uORFs), define its molecular and cellular functions, delineate downstream pathways (notably the ATF-4→cth-2→H2S axis), synthesize quantitative data on longevity and stress phenotypes, and highlight recent advances and translational implications. Where available, URLs and publication dates are provided; citations follow each claim.

Plan and verification
- Identity verification: The C. elegans gene symbol atf-4 corresponds to locus T04C10.4 and encodes a bZIP transcription factor, consistent with UniProt Q22156. Worm studies use atf-4(tm4397) mutants, a Patf-4(uORF)::GFP translational reporter, and Patf-4::ATF-4::GFP transgenes, confirming correct gene/protein identity in C. elegans (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9). The gene was previously referred to as atf-5 in some worm literature but corresponds to the ATF4 ortholog (statzer2022atf4andhydrogen pages 11-11, statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 4-5).

1) Key concepts and definitions
- atf-4 encodes a stress-inducible, nuclear bZIP transcription factor that functions as a central ISR effector in eukaryotes. In C. elegans, atf-4 (T04C10.4) is preferentially translated under reduced global protein synthesis and coordinates transcriptional programs that enhance proteostasis, stress resistance, and longevity (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 1-2, statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 4-5).
- ISR-linked translational control: atf-4 mRNA harbors two 5′ UTR uORFs that normally suppress main-ORF translation; when global initiation is reduced (e.g., by translation or mTORC1 inhibition), scanning ribosomes bypass uORF repression, selectively increasing ATF-4 synthesis. This was demonstrated using a Patf-4(uORF)::GFP reporter, ribosome profiling, and pharmacologic perturbations (cycloheximide, tunicamycin) (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 1-2, statzer2022atf4andhydrogen pages 4-4).

2) Recent developments and latest research (prioritized 2023–2024)
- Contemporary expert synthesis (2023): A review of ATF4 regulation and ISR outcomes consolidates mechanistic understanding of eIF2α kinase activation and the uORF-based translational logic that applies across species, informing interpretation of worm ATF-4 induction and target programs (Frontiers in Molecular Neuroscience; Feb 2023; https://doi.org/10.3389/fnmol.2023.1112253) (gotz2025suppressionratherthan pages 1-5).
- GCN2/ISR as a therapeutic axis (2024): A focused review highlights GCN2-eIF2α-ATF4 as a druggable node in age-related disease, reinforcing translational relevance of ATF-4 pathways uncovered in worms (Frontiers in Aging; Sep 2024; https://doi.org/10.3389/fragi.2024.1447370) (gotz2025suppressionratherthan pages 23-26, gotz2025suppressionratherthan pages 30-33).
- Although outside worms, these 2023–2024 sources align with worm mechanistic data and support the generalizability of ISR-ATF4 biology relevant to atf-4 (gotz2025suppressionratherthan pages 23-26, gotz2025suppressionratherthan pages 30-33, gotz2025suppressionratherthan pages 1-5).

3) Molecular function, localization, and pathway context in C. elegans
- Molecular function: ATF-4 acts as a transcriptional activator of cytoprotective and proteostasis genes. ATF-4 overexpression (Patf-4::ATF-4::GFP) upregulates small heat-shock/chaperone genes (e.g., sip-1/CRYAA, hsp-70, hsp-16.2, hsp-12.3) and other stress-response targets; several of these are required for ATF-4-driven lifespan extension, indicating a direct functional role in proteostasis (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 4-5).
- Subcellular localization: ATF-4::GFP localizes to nuclei in neuronal, hypodermal, and other somatic tissues upon overexpression, consistent with its role as a transcription factor acting in the nucleus (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 4-5).
- ISR and eIF2α: Tunicamycin robustly increases eIF2α phosphorylation and induces the atf-4 reporter and ATF-4 protein, whereas short cycloheximide treatment increases the atf-4 reporter with minimal eIF2α phosphorylation, indicating that reduced global translation alone can elevate ATF-4 translation. Notably, an eIF2α phosphorylation-defective mutant (y37e3.10(qd338)) still permits ifg-1(RNAi)-mediated, atf-4-dependent lifespan extension, establishing that some ATF-4 activation and longevity outputs can be ISR-independent in worms (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 4-4, statzer2022atf4andhydrogen pages 3-4).

4) Downstream pathways and gene programs
- ATF-4→cth-2→H2S axis: ATF-4 induces the transsulfuration enzyme cth-2, increasing hydrogen sulfide (H2S) production capacity and elevating protein persulfidation (PSSH), a protective cysteine modification. Genetic data show that cth-2 knockdown ablates longevity and stress resistance from mTORC1 pathway inhibition (e.g., raga-1), placing cth-2 downstream of ATF-4 in longevity control (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 8-9, statzer2022atf4andhydrogen pages 9-11).
- Network cooperation: ATF-4-driven longevity requires canonical longevity transcription factors—DAF-16/FOXO, HSF-1/HSF, and SKN-1/NRF—indicating interdependent transcriptional networks governing proteostasis and stress responses (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 4-5).

5) Roles in stress responses, immunity, and longevity, with quantitative data
- Longevity sufficiency: ATF-4 overexpression is sufficient to extend lifespan by approximately 7–44% across more than 10 independent trials and to improve healthspan (increased late-life pharyngeal pumping), establishing ATF-4 as a potent longevity factor in worms (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 4-5).
- Longevity necessity under translation suppression: Adult-specific reduction of global translation by ifg-1(RNAi) or short cycloheximide exposure extends lifespan in wild-type but not in atf-4 mutants, demonstrating that ATF-4 is required for longevity benefits from translation attenuation (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 4-4).
- Reporter induction and protein levels: Tunicamycin (35 μg/ml, 4 h) approximately doubles ATF-4 protein in L4 animals; atf-4 mRNA increases only ~1.5-fold, and induction of the Patf-4(uORF)::GFP reporter persists when transcription is blocked by α-amanitin, supporting translational control via uORFs (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 1-2).

6) Current applications and real-world implementations
- Pharmacologic triggers used in worms: Translation/ER stress modulators (cycloheximide and tunicamycin) and rapamycin (mTOR inhibitor) have been used to manipulate ATF-4 translation and/or reporter activity in C. elegans. Rapamycin increases the atf-4 uORF reporter, although rapamycin-induced lifespan extension can be ATF-4–independent in some contexts, indicating pathway- and context-specific roles (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 1-2, statzer2022atf4andhydrogen pages 4-4).
- Therapeutic implications: The worm ATF-4→cth-2→H2S pathway suggests that boosting H2S production or enhancing protein persulfidation could capture benefits of ISR/translation suppression without broad proteostasis disruption, consistent with translational interest in H2S donors under clinical investigation (as noted in the 2022 worm study) and reviews emphasizing ISR nodes as therapeutic targets (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9; Frontiers in Aging; Sep 2024; https://doi.org/10.3389/fragi.2024.1447370) (statzer2022atf4andhydrogen pages 11-11, gotz2025suppressionratherthan pages 23-26).

7) Expert opinions and integrative analysis
- Cross-species ISR logic: Reviews emphasize that eIF2α phosphorylation by stress-sensing kinases lowers global initiation while selectively enabling ATF4 translation via uORFs, a logic recapitulated by worm atf-4 reporters and ribosome profiling (Frontiers in Molecular Neuroscience; Feb 2023; https://doi.org/10.3389/fnmol.2023.1112253). Worm experiments further show that ATF-4 can be preferentially translated without detectable eIF2α phosphorylation under some translation-limiting conditions (e.g., ifg-1 depletion), underscoring parallel entry points into ATF-4 induction (gotz2025suppressionratherthan pages 1-5, statzer2022atf4andhydrogen pages 4-4).
- Longevity mechanisms: Worm data position ATF-4 as an integration node for translational and mTORC1 signals that converge on proteostasis (chaperones) and sulfur metabolism (cth-2/H2S), acting with DAF-16, HSF-1, and SKN-1 to enhance stress resistance and healthspan (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 4-5).

8) Summary statistics and data points
- Lifespan extension by ATF-4 overexpression: ~7–44% across >10 independent trials; improved late-life pumping (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 4-5).
- Reporter/protein induction under stress: Tunicamycin (35 μg/ml, 4 h) roughly doubles ATF-4 protein; atf-4 mRNA increases ~1.5×; cycloheximide (7.2 mM, 1 h) robustly increases the Patf-4(uORF)::GFP translational reporter (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 1-2).
- eIF2α phosphorylation: Strongly increased by tunicamycin; minimally affected by short cycloheximide, illustrating differential ISR engagement (Nature Communications; Feb 2022; https://doi.org/10.1038/s41467-022-28599-9) (statzer2022atf4andhydrogen pages 4-4).

Embedded summary table
| Area | Specific finding | Experimental support (methods/constructs) | Quantitative notes | Source (DOI/URL) | Date | Context ID |
|---|---|---|---|---|---|---|
| Identity | atf-4 (T04C10.4), 208 aa; bZIP transcription factor (ortholog of mammalian ATF4; formerly atf-5) | Gene/protein annotation and transgenic constructs: Patf-4::ATF-4::GFP (pWM48), atf-4(tm4397) mutant; reported protein length and locus information | — | https://doi.org/10.1038/s41467-022-28599-9 | Feb 2022 | (statzer2022atf4andhydrogen pages 11-11, statzer2022atf4andhydrogen pages 4-5) |
| ISR mechanism (uORF/eIF2α) | atf-4 contains two 5' UTR uORFs; preferential translation of main ORF when global translation is reduced; Patf-4(uORF)::GFP reporter induced post-transcriptionally (reporter induction persists with transcription blocked) | Patf-4(uORF)::GFP reporter (LD1499), ribosome profiling (SRA dataset), α-amanitin pre-treatment, puromycin incorporation assays | TM increased atf-4 mRNA ~1.5-fold; tunicamycin doubled ATF-4 protein; CHX (7.2 mM, 1 h) increased reporter; ifg-1 RNAi strongly increased reporter | https://doi.org/10.1038/s41467-022-28599-9 | Feb 2022 | (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 4-4, statzer2022atf4andhydrogen pages 1-2) |
| Roles in longevity & proteostasis | ATF-4 overexpression (ATF-4OE) is sufficient to extend lifespan and improve healthspan; upregulates small heat-shock/chaperone genes and proteostasis factors | ATF-4OE transgenic lines (wbmEx26, ldIs119), RNA-seq, qRT-PCR, Kaplan–Meier lifespan assays (with FUdR), pharyngeal pumping assays | Lifespan extension by ATF-4OE: ~7–44% across >10 trials; increased pharyngeal pumping at day 10; rapid increase in translation of atf-4 after heat shock | https://doi.org/10.1038/s41467-022-28599-9 | Feb 2022 | (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 4-5) |
| Downstream cth-2 / H2S axis & persulfidation | ATF-4 activates cth-2 (cystathionine γ-lyase) → increased H2S production capacity and elevated protein persulfidation (PSSH); cth-2 required for lifespan extension from mTORC1 inhibition | Genetic perturbations: raga-1, rict-1 RNAi/mutants; cth-2 knockdown/mutants; biochemical H2S production assays; persulfidation detection assays | cth-2 knockdown ablates raga-1(mediated) longevity; persulfidation levels increased with ATF-4OE and decreased in cth-2 or atf-4 mutants (statistical differences reported in paper figures) | https://doi.org/10.1038/s41467-022-28599-9 | Feb 2022 | (statzer2022atf4andhydrogen pages 8-9, statzer2022atf4andhydrogen pages 9-11) |
| Genetic dependencies & eIF2α note | ATF-4–driven longevity requires hsf-1, skn-1, and daf-16 (knockdown abolishes ATF-4OE benefit); however, some ATF-4 activation and lifespan effects from translation reduction can occur independently of canonical eIF2α phosphorylation | RNAi knockdowns (hsf-1, skn-1, daf-16), eif-2α phosphorylation-defective mutant y37e3.10(qd338), ifg-1 RNAi lifespan assays | Tunicamycin strongly increases eIF2α phosphorylation, but short CHX treatment did not; eif-2α(qd338) did not prevent lifespan extension caused by ifg-1 knockdown, indicating eIF2α-phospho–independent atf-4 activation routes | https://doi.org/10.1038/s41467-022-28599-9 | Feb 2022 | (statzer2022atf4andhydrogen pages 4-5, statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 4-4) |
| Subcellular localization (reporter) | ATF-4::GFP shows nuclear accumulation in neuronal, hypodermal and somatic tissues when overexpressed | Fluorescence imaging of Patf-4::ATF-4::GFP transgenics (ldIs119, wbmEx26) and Patf-4(uORF)::GFP reporter lines | Observed nuclear localization in multiple somatic tissues by GFP; reporter induction spatially resolved in imaging | https://doi.org/10.1038/s41467-022-28599-9 | Feb 2022 | (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 4-5) |
| Pharmacologic triggers & assays | Translation/ER stress modulators induce Patf-4 reporters and ATF-4 protein; rapamycin increases reporter but ATF-4 is not always required for rapamycin lifespan effects | Treatments: cycloheximide (CHX), tunicamycin (TM), rapamycin; puromycin incorporation to measure global translation; lifespan assays with drug treatments | CHX 7.2 mM (1 h) increases Patf-4 reporter; TM 35 µg/ml (4 h) doubled ATF-4 protein; puromycin assay used (0.5 mg/ml, 1 h) to measure translation changes; rapamycin increased reporter but rapamycin-mediated lifespan extension can be ATF-4–independent | https://doi.org/10.1038/s41467-022-28599-9 | Feb 2022 | (statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 1-2, statzer2022atf4andhydrogen pages 4-4) |

Table: Concise table of key, evidence-backed findings for C. elegans atf-4 (T04C10.4) from Statzer et al. (Nature Communications), including identity, ISR mechanism, functional roles, downstream H2S axis, genetic dependencies, localization, and pharmacologic triggers. Useful as a quick reference linking experimental methods, quantitative notes, DOI, date, and context IDs for follow-up.

Conclusions
C. elegans atf-4 (T04C10.4; bZIP) is a validated ATF4 ortholog that integrates translational and stress signals via uORF-mediated translational control to drive nuclear transcriptional programs enhancing proteostasis and longevity. A key downstream effector is cth-2, which elevates H2S production and protein persulfidation, and ATF-4 acts cooperatively with DAF-16, HSF-1, and SKN-1. ATF-4 sufficiency for lifespan extension (7–44%) and its necessity for longevity from translation suppression establish it as a central node in worm longevity circuits. Pharmacologic manipulation of translation, ER stress, or mTORC1 modulates ATF-4 reporters and phenotypes, suggesting translational potential for H2S-centric or ISR-targeted interventions. These findings provide a precise functional annotation of atf-4 in worms and a framework for targeted modulation in aging and stress biology (statzer2022atf4andhydrogen pages 8-9, statzer2022atf4andhydrogen pages 3-4, statzer2022atf4andhydrogen pages 1-2, statzer2022atf4andhydrogen pages 4-4, statzer2022atf4andhydrogen pages 4-5).

References

  1. (statzer2022atf4andhydrogen pages 11-11): Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William B. Mair, Alban Longchamp, Milos R. Filipovic, T. Keith Blackwell, and Collin Y. Ewald. Atf-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mtorc1. Nature Communications, Feb 2022. URL: https://doi.org/10.1038/s41467-022-28599-9, doi:10.1038/s41467-022-28599-9. This article has 84 citations and is from a highest quality peer-reviewed journal.

  2. (statzer2022atf4andhydrogen pages 3-4): Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William B. Mair, Alban Longchamp, Milos R. Filipovic, T. Keith Blackwell, and Collin Y. Ewald. Atf-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mtorc1. Nature Communications, Feb 2022. URL: https://doi.org/10.1038/s41467-022-28599-9, doi:10.1038/s41467-022-28599-9. This article has 84 citations and is from a highest quality peer-reviewed journal.

  3. (statzer2022atf4andhydrogen pages 4-5): Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William B. Mair, Alban Longchamp, Milos R. Filipovic, T. Keith Blackwell, and Collin Y. Ewald. Atf-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mtorc1. Nature Communications, Feb 2022. URL: https://doi.org/10.1038/s41467-022-28599-9, doi:10.1038/s41467-022-28599-9. This article has 84 citations and is from a highest quality peer-reviewed journal.

  4. (statzer2022atf4andhydrogen pages 1-2): Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William B. Mair, Alban Longchamp, Milos R. Filipovic, T. Keith Blackwell, and Collin Y. Ewald. Atf-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mtorc1. Nature Communications, Feb 2022. URL: https://doi.org/10.1038/s41467-022-28599-9, doi:10.1038/s41467-022-28599-9. This article has 84 citations and is from a highest quality peer-reviewed journal.

  5. (statzer2022atf4andhydrogen pages 4-4): Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William B. Mair, Alban Longchamp, Milos R. Filipovic, T. Keith Blackwell, and Collin Y. Ewald. Atf-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mtorc1. Nature Communications, Feb 2022. URL: https://doi.org/10.1038/s41467-022-28599-9, doi:10.1038/s41467-022-28599-9. This article has 84 citations and is from a highest quality peer-reviewed journal.

  6. (gotz2025suppressionratherthan pages 1-5): Miriam S Götz, Dan J. Hayman, Gracie Adams, Fumiaki Obata, and Mirre J P Simons. Suppression rather than activation of the integrated-stress-response (gcn2-atf4) pathway extends lifespan in the fly. BioRxiv, Jul 2025. URL: https://doi.org/10.1101/2025.07.14.664701, doi:10.1101/2025.07.14.664701. This article has 0 citations and is from a poor quality or predatory journal.

  7. (gotz2025suppressionratherthan pages 23-26): Miriam S Götz, Dan J. Hayman, Gracie Adams, Fumiaki Obata, and Mirre J P Simons. Suppression rather than activation of the integrated-stress-response (gcn2-atf4) pathway extends lifespan in the fly. BioRxiv, Jul 2025. URL: https://doi.org/10.1101/2025.07.14.664701, doi:10.1101/2025.07.14.664701. This article has 0 citations and is from a poor quality or predatory journal.

  8. (gotz2025suppressionratherthan pages 30-33): Miriam S Götz, Dan J. Hayman, Gracie Adams, Fumiaki Obata, and Mirre J P Simons. Suppression rather than activation of the integrated-stress-response (gcn2-atf4) pathway extends lifespan in the fly. BioRxiv, Jul 2025. URL: https://doi.org/10.1101/2025.07.14.664701, doi:10.1101/2025.07.14.664701. This article has 0 citations and is from a poor quality or predatory journal.

  9. (statzer2022atf4andhydrogen pages 8-9): Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William B. Mair, Alban Longchamp, Milos R. Filipovic, T. Keith Blackwell, and Collin Y. Ewald. Atf-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mtorc1. Nature Communications, Feb 2022. URL: https://doi.org/10.1038/s41467-022-28599-9, doi:10.1038/s41467-022-28599-9. This article has 84 citations and is from a highest quality peer-reviewed journal.

  10. (statzer2022atf4andhydrogen pages 9-11): Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William B. Mair, Alban Longchamp, Milos R. Filipovic, T. Keith Blackwell, and Collin Y. Ewald. Atf-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mtorc1. Nature Communications, Feb 2022. URL: https://doi.org/10.1038/s41467-022-28599-9, doi:10.1038/s41467-022-28599-9. This article has 84 citations and is from a highest quality peer-reviewed journal.

Citations

  1. gotz2025suppressionratherthan pages 1-5
  2. gotz2025suppressionratherthan pages 23-26
  3. gotz2025suppressionratherthan pages 30-33
  4. https://doi.org/10.1038/s41467-022-28599-9
  5. https://doi.org/10.3389/fnmol.2023.1112253
  6. https://doi.org/10.3389/fragi.2024.1447370
  7. https://doi.org/10.1038/s41467-022-28599-9;
  8. https://doi.org/10.1038/s41467-022-28599-9,
  9. https://doi.org/10.1101/2025.07.14.664701,

📄 View Raw YAML

id: Q22156
gene_symbol: atf-4
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: ATF-4 (also known as ATF-5) is a bZIP transcription factor and the 
  C. elegans ortholog of mammalian ATF4. It functions as a central effector of 
  the integrated stress response (ISR), being preferentially translated when 
  global protein synthesis is reduced due to eIF2alpha phosphorylation or other 
  translation-suppressing conditions. ATF-4 contains two upstream open reading 
  frames (uORFs) in its 5' UTR that normally suppress main-ORF translation; when
  ribosome initiation is slowed, these uORFs are bypassed, leading to increased 
  ATF-4 protein synthesis. ATF-4 localizes to the nucleus and acts as a 
  transcriptional activator, inducing expression of cytoprotective genes 
  including heat shock proteins (sip-1, hsp-70, hsp-16.2) and the 
  transsulfuration enzyme cth-2 (cystathionine gamma-lyase). The ATF-4/cth-2 
  axis increases hydrogen sulfide (H2S) production and protein persulfidation, 
  which are protective modifications that contribute to longevity and stress 
  resistance. ATF-4 overexpression extends lifespan by 7-44% and is required for
  longevity benefits from translation inhibition and mTORC1 suppression. 
  ATF-4-driven longevity requires the canonical longevity transcription factors 
  DAF-16/FOXO, HSF-1, and SKN-1/NRF.
existing_annotations:
  - term:
      id: GO:0000977
      label: RNA polymerase II transcription regulatory region sequence-specific
        DNA binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ATF-4 is a bZIP transcription factor that binds to DNA regulatory
        regions. The bZIP domain (residues 138-201) contains a basic motif 
        (residues 140-163) for DNA binding and a leucine zipper (residues 
        173-187) for dimerization. Phylogenetic inference from ATF4 orthologs 
        supports sequence-specific DNA binding activity. This is consistent with
        its function as a transcription factor that regulates target genes like 
        cth-2 and heat shock proteins [PMID:35181679].
      action: ACCEPT
      reason: IBA annotation is well-supported by domain architecture (bZIP with
        basic DNA-binding motif) and functional evidence that ATF-4 directly 
        regulates transcription of specific target genes including cth-2 and 
        heat shock proteins.
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: ATF-4 overexpression upregulated several small heat 
            shock protein (HSP) genes that are also controlled by HSF-1/HSF 
            (heat shock factor) and DAF-16/FOXO
        - reference_id: file:worm/atf-4/atf-4-deep-research-falcon.md
          supporting_text: 'model: Edison Scientific Literature'
  - term:
      id: GO:0001228
      label: DNA-binding transcription activator activity, RNA polymerase 
        II-specific
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ATF-4 functions as a transcriptional activator of cytoprotective 
        and proteostasis genes. Overexpression of ATF-4 upregulates expression 
        of target genes including cth-2 (cystathionine gamma-lyase), 
        sip-1/CRYAA, hsp-70, hsp-16.2, and hsp-12.3 [PMID:35181679]. This 
        demonstrates transcription activator function consistent with the 
        phylogenetically-inferred annotation.
      action: ACCEPT
      reason: Strong experimental support from PMID:35181679 demonstrating ATF-4
        positively regulates transcription of multiple target genes. IBA 
        annotation is phylogenetically sound and consistent with characterized 
        ATF4 function across species.
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: Each of the ATF-4-upregulated chaperone genes 
            sip-1/CRYAA, hsp-70/HSPA1L, hsp-16.2/HSPB1, and hsp-12.3/HSPB2 was 
            required for lifespan extension from ATF-4 overexpression
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: Nuclear localization is supported by phylogenetic inference and 
        is consistent with ATF-4's function as a transcription factor. The bZIP 
        domain contains basic residues typical of nuclear localization. Direct 
        experimental evidence is provided by IDA annotation from PMID:23692540 
        (see below).
      action: ACCEPT
      reason: IBA annotation is redundant with IDA evidence but correct. Nuclear
        localization is phylogenetically conserved and functionally required for
        transcription factor activity.
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: Transgenic ATF-4-overexpressing animals (ATF-4OE) 
            exhibited nuclear accumulation of ATF-4 in neuronal, hypodermal, and
            other somatic tissues under unstressed conditions
  - term:
      id: GO:0006357
      label: regulation of transcription by RNA polymerase II
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ATF-4 regulates RNA polymerase II-mediated transcription by 
        binding to regulatory elements and activating expression of target 
        genes. This is supported by experimental evidence showing ATF-4 
        overexpression increases transcription of target genes including cth-2, 
        sip-1, and heat shock proteins [PMID:35181679].
      action: ACCEPT
      reason: Well-supported IBA annotation consistent with ATF-4's established 
        role as a transcriptional regulator. The term appropriately captures the
        biological process without over-specifying.
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: ATF-4 overexpression upregulated several small heat 
            shock protein (HSP) genes that are also controlled by HSF-1/HSF 
            (heat shock factor) and DAF-16/FOXO
  - term:
      id: GO:0003677
      label: DNA binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: IEA annotation from UniProtKB keyword mapping. ATF-4 contains a 
        bZIP domain (IPR004827) with a basic DNA-binding motif (residues 
        140-163). This general term is subsumed by the more specific IBA 
        annotation for sequence-specific DNA binding (GO:0000977).
      action: ACCEPT
      reason: Correct but less specific than the IBA annotation for 
        sequence-specific DNA binding. The annotation is valid as it captures 
        the fundamental DNA-binding capability of the bZIP domain.
      supported_by:
        - reference_id: GO_REF:0000043
          supporting_text: '[Gene Ontology annotation based on UniProtKB/Swiss-Prot
            keyword mapping - DNA-binding keyword maps to GO:0003677]'
  - term:
      id: GO:0003700
      label: DNA-binding transcription factor activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: IEA annotation from InterPro record association. ATF-4 contains 
        the bZIP domain (IPR004827) which is associated with transcription 
        factor activity. This is consistent with ATF-4's characterized function 
        as a transcriptional activator.
      action: ACCEPT
      reason: Correct InterPro-based annotation. The bZIP domain definitively 
        establishes ATF-4 as a DNA-binding transcription factor, and 
        experimental evidence confirms this function.
      supported_by:
        - reference_id: GO_REF:0000002
          supporting_text: '[Gene Ontology annotation through association of InterPro
            records with GO terms - bZIP domain (IPR004827) associated with transcription
            factor activity]'
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: IEA annotation from UniProtKB subcellular location vocabulary 
        mapping. Nuclear localization is also supported by IDA (PMID:23692540) 
        and IBA evidence.
      action: ACCEPT
      reason: Correct annotation, redundant with IDA and IBA evidence. Nuclear 
        localization is well-established.
      supported_by:
        - reference_id: GO_REF:0000044
          supporting_text: '[Gene Ontology annotation based on UniProtKB/Swiss-Prot
            Subcellular Location vocabulary mapping]'
  - term:
      id: GO:0006351
      label: DNA-templated transcription
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: IEA annotation from keyword mapping indicating involvement in 
        transcription. ATF-4 participates in transcription as an activator, but 
        this general term is less informative than the more specific GO:0006357 
        (regulation of transcription by RNA polymerase II).
      action: ACCEPT
      reason: Valid but general annotation. ATF-4 participates in DNA-templated 
        transcription as a regulatory factor rather than as part of the core 
        transcription machinery.
      supported_by:
        - reference_id: GO_REF:0000043
          supporting_text: '[Gene Ontology annotation based on UniProtKB/Swiss-Prot
            keyword mapping - Transcription keyword]'
  - term:
      id: GO:0006355
      label: regulation of DNA-templated transcription
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: IEA annotation from InterPro association indicating 
        transcriptional regulatory function. This is appropriately general and 
        consistent with ATF-4's role as a transcription factor.
      action: ACCEPT
      reason: Correct annotation capturing ATF-4's regulatory role in 
        transcription. Consistent with more specific annotations for RNA 
        polymerase II transcription regulation.
      supported_by:
        - reference_id: GO_REF:0000002
          supporting_text: '[Gene Ontology annotation through association of InterPro
            records with GO terms - bZIP domain associated with transcription regulation]'
  - term:
      id: GO:0045944
      label: positive regulation of transcription by RNA polymerase II
    evidence_type: IEA
    original_reference_id: GO_REF:0000108
    review:
      summary: IEA annotation inferred from logical relationships. ATF-4 is 
        established as a transcriptional activator based on the IBA annotation 
        for GO:0001228 (DNA-binding transcription activator activity). 
        Experimental evidence from PMID:35181679 confirms ATF-4 overexpression 
        upregulates target gene expression.
      action: ACCEPT
      reason: Correct logical inference from transcription activator activity to
        positive regulation of transcription. Well-supported by experimental 
        evidence demonstrating ATF-4 activates transcription of target genes.
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: ATF-4 overexpression upregulated several small heat 
            shock protein (HSP) genes that are also controlled by HSF-1/HSF 
            (heat shock factor) and DAF-16/FOXO
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:23661758
    review:
      summary: This annotation derives from a large-scale study of bZIP 
        protein-protein interactions across species, measuring 2891 protein 
        pairs in vitro [PMID:23661758]. The study examined bZIP dimerization 
        networks and found extensive rewiring of interactions. While the 
        interaction data is valuable, the GO term "protein binding" is 
        uninformative and should be replaced with a more specific term 
        indicating bZIP dimerization.
      action: MODIFY
      reason: The annotation captures real protein-protein interactions, but 
        "protein binding" (GO:0005515) is too vague. ATF-4 dimerizes with other 
        bZIP proteins through its leucine zipper domain. A more informative term
        would be "DNA-binding transcription factor binding" (GO:0140297) or 
        annotation to a specific partner like CEBP-2 (documented in IntAct).
      proposed_replacement_terms:
        - id: GO:0140297
          label: DNA-binding transcription factor binding
      additional_reference_ids:
        - IntAct:EBI-6749607
      supported_by:
        - reference_id: PMID:23661758
          supporting_text: We studied the basic region-leucine zipper (bZIP) 
            transcription factors and quantified bZIP dimerization networks for 
            five metazoan and two single-cell species, measuring interactions in
            vitro for 2891 protein pairs
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:23791784
    review:
      summary: This annotation is from a comprehensive study of C. elegans 
        transcription factor networks that characterized interaction rewiring 
        after gene duplication [PMID:23791784]. The study examined 
        protein-protein and protein-DNA interactions across TF families. As with
        the other protein binding annotation, this term is too general.
      action: MODIFY
      reason: Valid interaction data but "protein binding" is uninformative. The
        study examined TF networks, so more specific terms describing 
        transcription factor complex formation or DNA-binding transcription 
        factor binding would be more appropriate.
      proposed_replacement_terms:
        - id: GO:0140297
          label: DNA-binding transcription factor binding
      supported_by:
        - reference_id: PMID:23791784
          supporting_text: we comprehensively characterize such network rewiring
            for C. elegans transcription factors (TFs) within and across four 
            newly delineated molecular networks
  - term:
      id: GO:0010628
      label: positive regulation of gene expression
    evidence_type: IMP
    original_reference_id: PMID:35181679
    review:
      summary: ATF-4 overexpression increases expression of multiple target 
        genes including cth-2 (cystathionine gamma-lyase), sip-1/CRYAA, hsp-70, 
        hsp-16.2, and hsp-12.3 as demonstrated by RNA-seq and qRT-PCR 
        [PMID:35181679]. Loss of atf-4 reduces expression of these targets. This
        IMP annotation is well-supported by the experimental evidence.
      action: ACCEPT
      reason: Strong experimental evidence from overexpression and 
        loss-of-function studies demonstrating ATF-4 positively regulates gene 
        expression. The annotation accurately captures ATF-4's transcriptional 
        activator function.
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: Each of the ATF-4-upregulated chaperone genes 
            sip-1/CRYAA, hsp-70/HSPA1L, hsp-16.2/HSPB1, and hsp-12.3/HSPB2 was 
            required for lifespan extension from ATF-4 overexpression
  - term:
      id: GO:0070814
      label: hydrogen sulfide biosynthetic process
    evidence_type: IMP
    original_reference_id: PMID:35181679
    review:
      summary: ATF-4 promotes hydrogen sulfide (H2S) biosynthesis by 
        transcriptionally activating cth-2 (cystathionine gamma-lyase), which 
        catalyzes H2S production in the transsulfuration pathway. ATF-4 
        overexpression increases H2S production capacity, while atf-4 loss 
        reduces it. The H2S pathway is required for ATF-4-mediated longevity 
        [PMID:35181679].
      action: ACCEPT
      reason: Strong experimental evidence demonstrating ATF-4 regulates H2S 
        biosynthesis through transcriptional activation of cth-2. This is a key 
        downstream effector pathway of ATF-4.
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: ATF-4 promotes longevity by activating canonical 
            anti-ageing mechanisms, but also by elevating expression of the 
            transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) 
            production
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IDA
    original_reference_id: PMID:23692540
    review:
      summary: Direct experimental observation of ATF-4 (referred to as ATF-5 in
        this publication) localization to the nucleus. The study examined GCN-2 
        and its downstream targets in the context of TOR signaling and 
        longevity. Nuclear localization is consistent with ATF-4's function as a
        transcription factor.
      action: ACCEPT
      reason: Primary experimental evidence (IDA) directly demonstrating nuclear
        localization. This is the strongest evidence code for this cellular 
        component annotation.
      additional_reference_ids:
        - PMID:35181679
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: Transgenic ATF-4-overexpressing animals (ATF-4OE) 
            exhibited nuclear accumulation of ATF-4 in neuronal, hypodermal, and
            other somatic tissues under unstressed conditions
  - term:
      id: GO:0140467
      label: integrated stress response signaling
    evidence_type: IMP
    original_reference_id: PMID:35181679
    review:
      summary: ATF-4 is a central effector of the integrated stress response 
        (ISR). It is preferentially translated when eIF2alpha is phosphorylated 
        or when global translation is suppressed. ATF-4 contains two uORFs in 
        its 5' UTR that mediate this translational control. The ISR pathway 
        converges on ATF-4 to activate cytoprotective gene programs 
        [PMID:35181679].
      action: NEW
      reason: This is a core function of ATF-4 that is not currently annotated. 
        The deep research clearly establishes ATF-4 as a key ISR effector, and 
        GO:0140467 specifically mentions ATF4 in its definition. This annotation
        should be added with IMP evidence.
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: ATF-4 is preferentially translated under conditions 
            of reduced global protein synthesis
  - term:
      id: GO:0008340
      label: determination of adult lifespan
    evidence_type: IMP
    original_reference_id: PMID:35181679
    review:
      summary: ATF-4 overexpression extends C. elegans lifespan by 7-44% across 
        multiple independent trials and improves healthspan metrics. Loss of 
        atf-4 abrogates longevity benefits from translation inhibition and 
        mTORC1 suppression. ATF-4 is both necessary and sufficient for lifespan 
        extension under specific conditions [PMID:35181679].
      action: NEW
      reason: Lifespan regulation is a major characterized function of ATF-4 in 
        C. elegans. The evidence is strong and direct 
        (overexpression/loss-of-function lifespan assays). This core function 
        should be annotated.
      supported_by:
        - reference_id: PMID:35181679
          supporting_text: ATF-4 overexpression is sufficient to increase 
            lifespan
references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with
      GO terms
    findings:
      - statement: ATF-4 bZIP domain (IPR004827) associated with transcription 
          factor activity
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings:
      - statement: Phylogenetic inference from ATF4 orthologs supports DNA 
          binding and transcription activator functions
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword 
      mapping
    findings:
      - statement: DNA-binding and Transcription keywords mapped to appropriate 
          GO terms
  - id: GO_REF:0000044
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular 
      Location vocabulary mapping
    findings:
      - statement: Nucleus localization from UniProt subcellular location 
          annotation
  - id: GO_REF:0000108
    title: Automatic assignment of GO terms using logical inference, based on 
      inter-ontology links
    findings:
      - statement: Positive regulation of transcription inferred from 
          transcription activator activity
  - id: PMID:23661758
    title: Networks of bZIP protein-protein interactions diversified over a 
      billion years of evolution.
    findings:
      - statement: Comprehensive analysis of bZIP dimerization networks across 
          species
        supporting_text: We studied the basic region-leucine zipper (bZIP) 
          transcription factors and quantified bZIP dimerization networks for 
          five metazoan and two single-cell species, measuring interactions in 
          vitro for 2891 protein pairs
      - statement: ATF-4 participates in heteromeric bZIP interactions
        supporting_text: Metazoans have a higher proportion of heteromeric bZIP 
          interactions and more network complexity than the single-cell species
  - id: PMID:23692540
    title: The general control nonderepressible-2 kinase mediates stress 
      response and longevity induced by target of rapamycin inactivation in 
      Caenorhabditis elegans.
    findings:
      - statement: GCN-2 kinase functions upstream of ATF-4 in stress response
      - statement: ATF-4 (referred to as ATF-5) mediates longevity from TOR 
          pathway inhibition
      - statement: Nuclear localization of ATF-4 demonstrated
    full_text_unavailable: true
  - id: PMID:23791784
    title: Extensive rewiring and complex evolutionary dynamics in a C. elegans 
      multiparameter transcription factor network.
    findings:
      - statement: Comprehensive characterization of C. elegans TF interaction 
          networks
        supporting_text: we comprehensively characterize such network rewiring 
          for C. elegans transcription factors (TFs) within and across four 
          newly delineated molecular networks
      - statement: ATF-4 participates in TF-TF interaction networks
        supporting_text: Gene duplication results in two identical paralogs that
          diverge through mutation, leading to loss or gain of interactions with
          other biomolecules
  - id: PMID:35181679
    title: ATF-4 and hydrogen sulfide signalling mediate longevity in response 
      to inhibition of translation or mTORC1.
    findings:
      - statement: ATF-4 is preferentially translated under reduced protein 
          synthesis conditions
        supporting_text: ATF-4 is preferentially translated under conditions of 
          reduced global protein synthesis
      - statement: ATF-4 contains two uORFs mediating translational control
        supporting_text: "The C. elegans atf-4 ortholog (previously named atf-5) contains
          two 5′ UTR uORFs"
      - statement: ATF-4 overexpression extends lifespan 7-44%
        supporting_text: ATF-4 overexpression increased lifespan by 7-44% across
          >10 independent trials
      - statement: ATF-4 activates cth-2 to increase H2S production
        supporting_text: ATF-4 promotes longevity by activating canonical 
          anti-ageing mechanisms, but also by elevating expression of the 
          transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) 
          production
      - statement: ATF-4 upregulates heat shock proteins (sip-1, hsp-70, 
          hsp-16.2, hsp-12.3)
        supporting_text: Each of the ATF-4-upregulated chaperone genes 
          sip-1/CRYAA, hsp-70/HSPA1L, hsp-16.2/HSPB1, and hsp-12.3/HSPB2 was 
          required for lifespan extension from ATF-4 overexpression
      - statement: ATF-4 localizes to nucleus in multiple somatic tissues
        supporting_text: Transgenic ATF-4-overexpressing animals (ATF-4OE) 
          exhibited nuclear accumulation of ATF-4 in neuronal, hypodermal, and 
          other somatic tissues under unstressed conditions
      - statement: ATF-4-driven longevity requires DAF-16, HSF-1, and SKN-1
        supporting_text: Each of those transcription factors is critical for 
          lifespan extension arising from suppression of translation10,11, and 
          we determined that they are also needed for longevity conferred by 
          ATF-4 overexpression
      - statement: ATF-4 increases protein persulfidation through cth-2/H2S 
          pathway
        supporting_text: This H2S boost increases protein persulfidation, a 
          protective modification of redox-reactive cysteines
  - id: file:worm/atf-4/atf-4-deep-research-falcon.md
    title: Deep research findings on atf-4 gene function
    findings:
      - statement: ATF-4 is a validated ATF4 ortholog that integrates 
          translational and stress signals via uORF-mediated translational 
          control
core_functions:
  - description: ATF-4 is a bZIP transcription factor that activates expression 
      of target genes including cth-2, sip-1, hsp-70, hsp-16.2, and hsp-12.3. 
      Overexpression increases target gene expression; loss-of-function reduces 
      it [PMID:35181679].
    molecular_function:
      id: GO:0001228
      label: DNA-binding transcription activator activity, RNA polymerase 
        II-specific
    directly_involved_in:
      - id: GO:0140467
        label: integrated stress response signaling
      - id: GO:0045944
        label: positive regulation of transcription by RNA polymerase II
    locations:
      - id: GO:0005634
        label: nucleus
    supported_by:
      - reference_id: PMID:35181679
        supporting_text: Each of the ATF-4-upregulated chaperone genes 
          sip-1/CRYAA, hsp-70/HSPA1L, hsp-16.2/HSPB1, and hsp-12.3/HSPB2 was 
          required for lifespan extension from ATF-4 overexpression
  - description: ATF-4 promotes H2S biosynthesis by transcriptionally activating
      cth-2 (cystathionine gamma-lyase). The ATF-4/cth-2/H2S axis is required 
      for longevity from mTORC1 inhibition and increases protective protein 
      persulfidation [PMID:35181679].
    molecular_function:
      id: GO:0001228
      label: DNA-binding transcription activator activity, RNA polymerase 
        II-specific
    directly_involved_in:
      - id: GO:0070814
        label: hydrogen sulfide biosynthetic process
      - id: GO:0008340
        label: determination of adult lifespan
    locations:
      - id: GO:0005634
        label: nucleus
    supported_by:
      - reference_id: PMID:35181679
        supporting_text: ATF-4 promotes longevity by activating canonical 
          anti-ageing mechanisms, but also by elevating expression of the 
          transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) 
          production
proposed_new_terms: []
suggested_questions:
  - question: What are the specific DNA binding sites/motifs recognized by C. 
      elegans ATF-4? Are they canonical CRE (cAMP response element) sites or 
      different from mammalian ATF4?
    experts:
      - T. Keith Blackwell
      - Collin Y. Ewald
  - question: Does ATF-4 form heterodimers with specific bZIP partners in vivo, 
      and do these partnerships affect target gene specificity?
    experts:
      - Amy E. Keating
      - Albertha J. Walhout
  - question: What is the relative contribution of eIF2alpha-dependent vs. 
      eIF2alpha-independent mechanisms to ATF-4 translation under different 
      stress conditions?
    experts:
      - William B. Mair
      - Cole Haynes
suggested_experiments:
  - description: ChIP-seq for ATF-4 to identify genome-wide binding sites and 
      characterize the DNA motifs recognized by C. elegans ATF-4. This would 
      definitively establish direct ATF-4 targets and allow comparison to 
      mammalian ATF4 binding preferences.
    hypothesis: ATF-4 binds to canonical CRE or related motifs in promoters of 
      target genes like cth-2 and heat shock proteins.
    experiment_type: ChIP-seq
  - description: Tissue-specific rescue experiments to determine which tissues 
      require ATF-4 for longevity (neuronal vs. intestinal vs. hypodermal). 
      ATF-4 is expressed in multiple tissues; identifying the key tissue(s) for 
      lifespan effects would inform the mechanism.
    hypothesis: ATF-4 acts in specific tissues (likely neurons or intestine) to 
      coordinate organism-wide stress responses and longevity.
    experiment_type: Tissue-specific rescue
tags:
  - caeel-upr-stress