GCN-2 is the sole C. elegans homolog of yeast/mammalian GCN2, a serine/threonine protein kinase that phosphorylates eIF2alpha at Ser49 in response to amino acid deprivation, mitochondrial stress, osmotic stress, and oxidative stress. It is the primary sensor for the integrated stress response (ISR) in C. elegans alongside PEK-1 (PERK homolog). GCN-2 functions to attenuate global translation while enabling selective translation of stress-responsive mRNAs such as atf-5, pha-4, and gpdh-1. It is required for lifespan extension associated with dietary restriction and TOR inhibition, and protects against mitochondrial dysfunction through translational control complementary to ATFS-1-mediated chaperone induction.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation inferred from phylogenetic analysis. While GCN-2 primarily functions in the cytosol at ribosome-associated sites, studies in other organisms show GCN2 can localize to nucleus. However, direct localization data for C. elegans GCN-2 in the nucleus was not found in retrieved literature (Tatara et al. 2024). Reason: Phylogenetic inference is reasonable given conservation of GCN2 across eukaryotes. Nuclear localization is plausible though not directly demonstrated in C. elegans. Accept as IBA represents well-curated phylogenetic evidence. Supporting Evidence: file:worm/gcn-2/gcn-2-deep-research-falcon.md model: Edison Scientific Literature |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for cytoplasmic localization. GCN-2 functions in the cytosol at ribosome-associated sites through GCN1/ABCF complexes binding to polyribosomes and collided ribosomes (Tatara et al. 2024, Altintas et al. 2024). Reason: Cytoplasmic localization is well-established for GCN2 family kinases. The protein functions at ribosomes in the cytosol to phosphorylate eIF2alpha. Supporting Evidence: DOI:10.3390/ijms25052998 GCN1 is the ribosome-associated activator of GCN-2... bind polyribosomes and stalled/disome ribosomes |
| GO:0034198 cellular response to amino acid starvation | IBA GO_REF:0000033 | ACCEPT | Summary: Core function of GCN-2. The kinase responds to amino acid limitation by phosphorylating eIF2alpha. This was directly demonstrated in C. elegans by Rousakis et al. 2013, showing GCN-2-dependent eIF2alpha phosphorylation when aminoacyl-tRNA synthetases are knocked down (PMID:23692540). Reason: This is the primary, evolutionarily conserved function of GCN2 kinases. Directly demonstrated in C. elegans with RNAi of tRNA synthetases (krs-1, lrs-1). Supporting Evidence: PMID:23692540 We found that worms grown on bacteria expressing dsRNA for krs-1 either arrested in early larval stages or became adults with low brood size |
| GO:0032057 negative regulation of translational initiation in response to stress | IBA GO_REF:0000033 | ACCEPT | Summary: Core function of GCN-2. Phosphorylation of eIF2alpha by GCN-2 attenuates global translation initiation. Directly demonstrated in C. elegans during mitochondrial stress (Baker et al. 2012), osmotic stress (Lee & Strange 2012), and amino acid limitation (Rousakis et al. 2013). Reason: Well-established mechanism of GCN2 function across species and directly demonstrated in C. elegans. Supporting Evidence: PMID:22719267 GCN-2-dependent eIF2alpha phosphorylation is required for development as well as the lifespan extension observed in Caenorhabditis elegans PMID:23076791 Hypertonicity-induced translation inhibition is mediated by general control nonderepressible (GCN)-2 kinase signaling and eIF-2alpha phosphoryation |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for cytosolic localization. GCN-2 functions in the cytosol at ribosome-associated sites. More specific than GO:0005737 (cytoplasm). Reason: Consistent with known localization of GCN2 kinases functioning at cytosolic ribosomes. IBA represents well-curated phylogenetic evidence. |
| GO:0004694 eukaryotic translation initiation factor 2alpha kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Core molecular function of GCN-2. Directly demonstrated in C. elegans by multiple studies showing GCN-2-dependent phosphorylation of eIF2alpha at Ser49 (Baker et al. 2012, Lee & Strange 2012, Rousakis et al. 2013). Reason: This is the defining enzymatic activity of GCN-2. Directly demonstrated in C. elegans by immunoblotting with phospho-specific antibodies. Supporting Evidence: PMID:22719267 in a deletion mutant lacking 1482 bases of gcn-2 (gcn-2(ok871)), the level of steady-state phospho-eIF2alpha was reduced relative to wild-type worms PMID:23692540 By measuring the basal levels of eIF2alpha phosphorylation in whole protein extracts of N2 worms subjected to gcn-2(RNAi)... we verified that both ok871 and ok886 are loss-of-function alleles of gcn-2 |
| GO:0000166 nucleotide binding | IEA GO_REF:0000043 | ACCEPT | Summary: IEA based on UniProt keyword mapping. GCN-2 is an ATP-dependent kinase. The protein contains ATP binding sites at positions 114-122, 154, 497-505, and 520 per UniProt annotation. Reason: Correct but generic. GCN-2 requires ATP for kinase activity. More specific annotations exist (GO:0005524 ATP binding). |
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | ACCEPT | Summary: IEA based on InterPro domain mapping. GCN-2 belongs to the protein kinase superfamily with two protein kinase domains (positions 108-507 and 508-999). Reason: Correct but generic. More specific term GO:0004694 (eIF2alpha kinase activity) is also annotated and is more informative. |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA based on combined automated annotation. GCN-2 is a serine/threonine kinase that phosphorylates eIF2alpha on serine residue (Ser49 in C. elegans, equivalent to Ser51 in mammals). Reason: Correct. GCN-2 specifically phosphorylates serine residues. More specific term GO:0004694 is also present. |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: IEA based on combined automated annotation. GCN-2 contains an ATP binding site in its kinase domain and requires ATP for catalytic activity. Reason: Correct. GCN-2 is an ATP-dependent kinase with conserved ATP-binding sites. |
| GO:0006417 regulation of translation | IEA GO_REF:0000043 | ACCEPT | Summary: IEA based on UniProt keyword. GCN-2 regulates translation by phosphorylating eIF2alpha, which reduces global translation while enabling preferential translation of uORF-containing mRNAs. Reason: Correct but generic. More specific annotations exist for negative regulation of translational initiation in response to stress. |
| GO:0006986 response to unfolded protein | IEA GO_REF:0000043 | ACCEPT | Summary: IEA based on UniProt keyword. GCN-2 is involved in the integrated stress response which includes unfolded protein response. UniProt function annotation states GCN-2 is "Involved in the unfolded protein response (UPR) triggered by several stresses including mitochondrial, osmotic and oxidative stresses." Reason: Supported by UniProt annotation and consistent with GCN-2 role in ISR. However, PEK-1 (PERK) is the primary UPR-ER sensor in C. elegans. Supporting Evidence: PMID:20733002 GCN-2, which is known to suppress translation and induce an adaptive transcriptional response under conditions of UPR activation or amino acid deprivation, was required for HP |
| GO:0009893 positive regulation of metabolic process | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: IEA based on ARBA machine learning. This is a very broad term. GCN-2 does influence metabolic processes through translational reprogramming. Reason: Too broad to be informative for this specific kinase. The more specific processes regulated by GCN-2 (translation, stress response) are annotated separately. |
| GO:0010468 regulation of gene expression | IEA GO_REF:0000117 | ACCEPT | Summary: IEA based on ARBA machine learning. GCN-2 regulates gene expression at the translational level and indirectly at the transcriptional level through ATF-5/ATF4 induction. Reason: Correct but broad. GCN-2 regulates gene expression through translational control and induction of transcription factors like ATF-5 and PHA-4. Supporting Evidence: PMID:23692540 Phosphorylation of eIF2alpha under stress results in inhibition of global protein synthesis, which is accompanied by favored translation of specific mRNAs that adapt the organism to stress |
| GO:0016301 kinase activity | IEA GO_REF:0000043 | ACCEPT | Summary: IEA based on UniProt keyword mapping. GCN-2 is a kinase. Very broad term. Reason: Correct but very generic. More specific kinase activity terms are annotated. |
| GO:0016740 transferase activity | IEA GO_REF:0000043 | ACCEPT | Summary: IEA based on UniProt keyword mapping. Kinases are transferases that transfer phosphate groups. Reason: Correct but extremely generic. Acceptable as it is captured by automated hierarchy but more specific terms are more informative. |
| GO:0033554 cellular response to stress | IEA GO_REF:0000117 | ACCEPT | Summary: IEA based on ARBA machine learning. GCN-2 is activated by multiple stresses including amino acid starvation, mitochondrial stress, osmotic stress, and oxidative stress. Reason: Correct. GCN-2 is a central kinase in cellular stress response pathways. Supporting Evidence: PMID:23692540 GCN-2 signaling positively regulates the induction of PHA-4/FoxA transcription factor under nutrient or oxidative stress, as part of the adaptive response that ensures stress survival and longevity |
| GO:0051246 regulation of protein metabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: IEA based on ARBA machine learning. GCN-2 regulates protein metabolism through translational control. Reason: Correct. GCN-2 regulates protein synthesis rates through eIF2alpha phosphorylation. |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | ACCEPT | Summary: IEA based on Rhea mapping. GCN-2 phosphorylates serine residues, specifically Ser49 of eIF2alpha. Reason: Correct. The catalytic reaction phosphorylates serine residues. |
| GO:0140469 GCN2-mediated signaling | IMP PMID:20733002 Protein misfolding induces hypoxic preconditioning via a sub... | ACCEPT | Summary: IMP annotation from Mao & Crowder 2010 study on hypoxic preconditioning. The study shows GCN-2 is required for hypoxic preconditioning (HP) through a mechanism involving IRE-1 but not XBP-1 or ATF-6. Reason: Direct experimental evidence that GCN-2 functions in GCN2-mediated signaling in C. elegans during hypoxic stress response. Supporting Evidence: PMID:20733002 HP also required IRE-1 but not XBP-1 or ATF-6; instead, GCN-2, which is known to suppress translation and induce an adaptive transcriptional response under conditions of UPR activation or amino acid deprivation, was required for HP |
| GO:0140469 GCN2-mediated signaling | IMP PMID:22719267 Protective coupling of mitochondrial function and protein sy... | ACCEPT | Summary: IMP annotation from Baker et al. 2012. Study demonstrates GCN-2 functions in the mitochondrial unfolded protein response through eIF2alpha phosphorylation, complementary to ATFS-1-mediated chaperone induction. Reason: Strong experimental evidence for GCN-2 signaling during mitochondrial stress. Uses gcn-2(ok871) deletion mutant. Supporting Evidence: PMID:22719267 GCN-2-dependent translational control acts in a mitochondrial protective signaling pathway complementary to the regulation of mitochondrial chaperone gene expression mediated by HAF-1 and ATFS-1 |
| GO:0140469 GCN2-mediated signaling | IMP PMID:23692540 The general control nonderepressible-2 kinase mediates stres... | ACCEPT | Summary: IMP annotation from Rousakis et al. 2013. Comprehensive study establishing conserved GCN-2 function in amino acid sensing and its role in stress response and longevity. Reason: Strong experimental evidence using gcn-2 mutants (ok871 and ok886) demonstrating GCN-2 signaling in C. elegans. Supporting Evidence: PMID:23692540 we have established the conserved function of the GCN-2 kinase in C. elegans under amino acid limitation, and we showed that loss of GCN-2 activity is not required for normal lifespan, but affects the lifespan of nutrient-sensitized worms |
| GO:1904688 regulation of cytoplasmic translational initiation | IGI PMID:22719267 Protective coupling of mitochondrial function and protein sy... | ACCEPT | Summary: IGI annotation from Baker et al. 2012. The study shows genetic interaction between gcn-2 and gsp-1 (phosphatase) in regulating eIF2alpha phosphorylation and translation. Reason: Valid genetic interaction evidence. gsp-1(RNAi) increases phospho-eIF2alpha while gcn-2 deletion reduces it, demonstrating opposing roles in regulating cytoplasmic translation initiation. Supporting Evidence: PMID:22719267 In contrast to inhibition of GCN-2 and PEK-1, GSP-1 knockdown resulted in increased levels of phospho-eIF2alpha consistent with it acting as a constitutive eIF2alpha phosphatase |
| GO:1904688 regulation of cytoplasmic translational initiation | IMP PMID:23692540 The general control nonderepressible-2 kinase mediates stres... | ACCEPT | Summary: IMP annotation from Rousakis et al. 2013. Study directly demonstrates GCN-2 regulates translation initiation through eIF2alpha phosphorylation. Reason: Direct evidence from gcn-2 mutant analysis showing loss of eIF2alpha phosphorylation and translational regulation. Supporting Evidence: PMID:23692540 Inhibition of protein synthesis is attained through phosphorylation of the alpha subunit of the translation initiation factor 2 (eIF2alpha) by specific protein kinases |
| GO:0010628 positive regulation of gene expression | IMP PMID:23076791 GCN-2 dependent inhibition of protein synthesis activates os... | ACCEPT | Summary: IMP annotation from Lee & Strange 2012. Study shows GCN-2 positively regulates gpdh-1 transcription during osmotic stress through WNK and Ste20 kinase signaling downstream of eIF2alpha phosphorylation. Reason: Direct experimental evidence that GCN-2 activity leads to induction of osmoprotective gene transcription. Supporting Evidence: PMID:23076791 GCN-2 dependent inhibition of protein synthesis activates osmosensitive gene transcription via WNK and Ste20 kinase signaling |
| GO:0034514 mitochondrial unfolded protein response | IMP PMID:22719267 Protective coupling of mitochondrial function and protein sy... | ACCEPT | Summary: IMP annotation from Baker et al. 2012. This landmark study demonstrates GCN-2 functions in the UPRmt as a complementary arm to ATFS-1-mediated chaperone induction. ROS from dysfunctional mitochondria activate GCN-2-dependent eIF2alpha phosphorylation. Reason: Strong experimental evidence establishing GCN-2 role in UPRmt. Uses clk-1 and isp-1 mitochondrial mutants with gcn-2(ok871). Supporting Evidence: PMID:22719267 Reactive oxygen species (ROS) generated from dysfunctional mitochondria are required for GCN-2-dependent eIF2alpha phosphorylation but not ATFS-1 activation PMID:22719267 Simultaneous deletion of ATFS-1 and GCN-2 compounds the developmental defects associated with mitochondrial stress |
| GO:0034063 stress granule assembly | IMP PMID:25061667 Diverse functions of mRNA metabolism factors in stress defen... | ACCEPT | Summary: IMP annotation from Rousakis et al. 2014. The study examines stress granule formation in C. elegans and shows GCN-2-dependent stress granule formation under certain stress conditions. The study shows SG formation depends on translation inhibition pathways including GCN-2 signaling. Reason: Experimental evidence linking GCN-2 to stress granule assembly. GCN-2 inhibits translation initiation, which is required for stress granule formation. Supporting Evidence: PMID:25061667 Both complexes were accumulated in response to various stress conditions, but distinct modes of SG formation were induced, depending on the insult |
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Download this section (compressed HTML)Q: Does C. elegans GCN-2 have substrates other than eIF2alpha that contribute to dietary restriction-induced lifespan extension?
Q: What is the mechanism by which ROS activate GCN-2 in C. elegans?
Q: Is there tissue-specific expression or function of GCN-2 in C. elegans?
Experiment: Direct localization studies of endogenous GCN-2 in C. elegans tissues using CRISPR-tagged GCN-2 or specific antibodies
Hypothesis: GCN-2 localizes primarily to the cytosol in association with ribosomes
Experiment: Phosphoproteomics analysis of gcn-2 mutants to identify potential non-eIF2alpha substrates of GCN-2
Hypothesis: GCN-2 may have additional substrates beyond eIF2alpha that contribute to stress responses
Experiment: Tissue-specific rescue experiments in gcn-2 mutants to determine site of action for lifespan and stress resistance phenotypes
Hypothesis: GCN-2 function in specific tissues (e.g., intestine, neurons) is critical for organismal stress responses
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