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.
| 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). Proposed replacements: DNA-binding transcription factor binding 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. Proposed replacements: DNA-binding transcription factor binding 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 |
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Download this section (compressed HTML)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
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
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