Gcn2 is the sole eIF2alpha kinase of Saccharomyces cerevisiae and the sensor kinase of the general amino acid control (GAAC), the yeast form of the integrated stress response. It is a large multidomain protein with an N-terminal RWD domain that binds the activator Gcn1 (in the Gcn1-Gcn20 complex), a pseudokinase domain, the protein kinase domain, a histidyl-tRNA synthetase-like domain and a C-terminal domain that mediates dimerization and ribosome binding. Gcn2 is a constitutive dimer that associates loosely with translating ribosomes in the cytosol. When amino acids (or purines, or glucose) are limiting, uncharged tRNAs accumulate and, delivered with the help of Gcn1 at the ribosomal A site, bind the HisRS-like and C-terminal domains; this relieves autoinhibition of the kinase domain, which trans-autophosphorylates its activation loop (Thr882/Thr887) and phosphorylates eIF2alpha (Sui2) on Ser51 (Ser52 in UniProt numbering). Phosphorylated eIF2 inhibits its guanine nucleotide exchange factor eIF2B, lowering ternary complex levels; global translation initiation falls while ribosomes bypass the inhibitory uORFs of GCN4 mRNA, so Gcn4 is translated and activates amino acid biosynthetic genes. Gcn2 activity is restrained by eEF1A and Yih1 and it also phosphorylates the TORC1 subunit Kog1 to down-regulate TORC1 during starvation. It has additional reported roles in a G1/S delay after DNA damage.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000049 tRNA binding | IDA PMID:10983975 Uncharged tRNA activates GCN2 by displacing the protein kina... | ACCEPT | Summary: Gcn2 binds several deacylated tRNAs through its bipartite HisRS-like plus C-terminal domain; this is the starvation-sensing input that activates the kinase. Reason: Direct binding assays show tRNA binding, weakened by aminoacylation. Uncharged-tRNA binding is the core sensing step of GCN2 activation, so this MF is part of its core function. Supporting Evidence: PMID:10983975 GCN2 bound several deacylated tRNAs with similar affinities, and aminoacylation of tRNAphe weakened its interaction with GCN2. file:yeast/GCN2/GCN2-uniprot.txt Binds uncharged tRNAs (PubMed:10983975, PubMed:7623840). |
| GO:0000049 tRNA binding | IDA PMID:7623840 The histidyl-tRNA synthetase-related sequence in the eIF-2 a... | ACCEPT | Summary: Northwestern assays showed uncharged tRNA binding to the HisRS-related domain of Gcn2. Reason: Independent direct-binding evidence for the tRNA-sensing function; core. Supporting Evidence: PMID:7623840 Using a Northwestern blot (RNA binding) assay, we show that uncharged tRNA can bind to the synthetase-related domain of GCN2. |
| GO:0000049 tRNA binding | IMP PMID:7623840 The histidyl-tRNA synthetase-related sequence in the eIF-2 a... | ACCEPT | Summary: Motif 2 mutations in the HisRS-related domain impair tRNA binding and abolish eIF2 phosphorylation. Reason: Mutational evidence ties tRNA binding to kinase activation; consistent with the IDA rows. Supporting Evidence: PMID:7623840 Mutations in the motif 2 sequence conserved among class II synthetases, including histidyl-tRNA synthetases, impair the ability of this synthetase-related domain to bind tRNA and abolish GCN2 phosphorylation of eIF-2 required to stimulate the general amino acid control response. |
| GO:0000077 DNA damage checkpoint signaling | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Electronic (ARBA/InterPro Gcn2 family) annotation to DNA damage checkpoint signaling. Reason: Yeast Gcn2 has experimental support for a G1/S checkpoint delay after DNA damage (PMID:17890903, IMP row), so the term holds for this gene, but it is peripheral to the amino-acid starvation kinase function. Kept as non-core, consistent with the IMP row. Supporting Evidence: PMID:17890903 Gcn2p regulates a G1/S cell cycle checkpoint in response to DNA damage. |
| GO:0000077 DNA damage checkpoint signaling | IMP PMID:17890903 Gcn2p regulates a G1/S cell cycle checkpoint in response to ... | KEEP AS NON CORE | Summary: gcn2 mutants are defective in a G1/S delay after DNA damage. Reason: The cached record has only the title; SGD curators read the full paper and the SGD description also says Gcn2 contributes to DNA damage checkpoint control. Defer to the curator but treat as non-core, since the mechanism probably runs through eIF2alpha phosphorylation rather than checkpoint signaling proper. Supporting Evidence: PMID:17890903 Gcn2p regulates a G1/S cell cycle checkpoint in response to DNA damage. file:yeast/GCN2/GCN2-deep-research-sgd.md contributes to DNA damage checkpoint control |
| GO:0003725 double-stranded RNA binding | IDA PMID:9430731 Ribosome-binding domain of eukaryotic initiation factor-2 ki... | KEEP AS NON CORE | Summary: The C-terminal ribosome-binding segment (residues 1467-1590), which resembles a DRBD core, binds dsRNA in vitro. Reason: Real in vitro activity of an isolated fragment, interpreted by the authors as a proxy for rRNA contacts that target Gcn2 to ribosomes. The physiological activity is ribosome binding (accepted separately); dsRNA binding is kept as non-core. Supporting Evidence: PMID:9430731 recombinant protein containing GCN2 residues 1467-1590 can bind double-stranded RNA in vitro, suggesting that interaction with rRNA mediates ribosome targeting |
| GO:0004672 protein kinase activity | IDA PMID:10983975 Uncharged tRNA activates GCN2 by displacing the protein kina... | MODIFY | Summary: Gcn2 kinase activity measured in vitro. Reason: Correct but general. The specific, well-established activity is eIF2alpha kinase activity (GO:0004694), which the gene already carries by IDA and IBA. Proposed replacements: eukaryotic translation initiation factor 2alpha kinase activity Supporting Evidence: PMID:10983975 Protein kinase GCN2 regulates translation in amino acid-starved cells by phosphorylating elF2. |
| GO:0004672 protein kinase activity | IDA PMID:2188100 Identification of positive-acting domains in GCN2 protein ki... | MODIFY | Summary: Kinase-dead K559 substitution abolished autophosphorylation and in vivo function. Reason: Correct but general; the physiological substrate is eIF2alpha, so GO:0004694 is the precise term. Proposed replacements: eukaryotic translation initiation factor 2alpha kinase activity Supporting Evidence: PMID:2188100 Substitution of a highly conserved lysine residue in the kinase domain abolished GCN2 regulatory function in vivo and its ability to autophosphorylate in vitro, indicating that GCN2 acts as a protein kinase in stimulating GCN4 expression. |
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro Ser/Thr kinase active-site mapping. Reason: Correct but general; refine to eIF2alpha kinase activity as for the experimental rows. Proposed replacements: eukaryotic translation initiation factor 2alpha kinase activity Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. GCN2 subfamily. |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000003 | MODIFY | Summary: EC 2.7.11.1 mapping to protein serine/threonine kinase activity. Reason: Correct but general; GO:0004694 is an is_a descendant and is the established activity. Proposed replacements: eukaryotic translation initiation factor 2alpha kinase activity Supporting Evidence: PMID:1739968 In vitro, GCN2 specifically phosphorylates the alpha subunit of rabbit or yeast eIF-2. |
| GO:0004694 eukaryotic translation initiation factor 2alpha kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBD at PTN000867953 (GCN2 clade), seeded by GCN2 orthologs including yeast GCN2 itself. Reason: The defining activity of the GCN2 clade; yeast GCN2 has its own direct evidence, and its presence among the seeds marks that grounding. Supporting Evidence: PMID:1739968 In vitro, GCN2 specifically phosphorylates the alpha subunit of rabbit or yeast eIF-2. |
| GO:0004694 eukaryotic translation initiation factor 2alpha kinase activity | IDA PMID:1739968 Phosphorylation of initiation factor 2 alpha by protein kina... | ACCEPT | Summary: Gcn2 phosphorylates eIF2alpha Ser51 in vitro and in vivo; the S51A mutation abolishes GCN4 induction. Reason: Founding direct evidence for the core activity. Supporting Evidence: PMID:1739968 Substitution of Ser-51 with alanine eliminates phosphorylation of eIF-2 alpha by GCN2 in vivo and in vitro and abolishes increased expression of GCN4 and amino acid biosynthetic genes under its control in amino acid-starved cells. |
| GO:0004694 eukaryotic translation initiation factor 2alpha kinase activity | IDA PMID:8798780 Histidyl-tRNA synthetase-related sequences in GCN2 protein k... | ACCEPT | Summary: In vitro eIF2alpha phosphorylation assay with recombinant yeast eIF2alpha, dependent on Ser51 and Gcn2 kinase activity. Reason: Direct biochemical evidence for the core activity. Supporting Evidence: PMID:8798780 Phosphorylation of the recombinant eIF-2alpha substrate was dependent on both GCN2 kinase activity and the eIF-2alpha phosphorylation site, serine 51. |
| GO:0004694 eukaryotic translation initiation factor 2alpha kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation from the Gcn2 InterPro family. Reason: Agrees with the experimental and IBA rows. Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt Metabolic-stress sensing protein kinase that phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (eIF-2-alpha/SUI2) on 'Ser-52' in response to low amino acid, carbon, or purine availability |
| GO:0004860 protein kinase inhibitor activity | IMP PMID:28057755 General Control Nonderepressible 2 (GCN2) Kinase Inhibits Ta... | MODIFY | Summary: In starved cells Gcn2 binds TORC1 and phosphorylates its regulatory subunit Kog1, lowering TORC1 activity; in gcn2 mutants TORC1 signaling is elevated and unresponsive to starvation. Reason: The finding (Gcn2 down-regulates TORC1) is sound, but the mechanism reported is phosphorylation of Kog1 by Gcn2 kinase activity, not a non-catalytic inhibitor activity. GO represents a kinase that inhibits its target by phosphorylation with the kinase activity (protein serine kinase activity, already on this gene) plus the regulated process. The process is negative regulation of TORC1 signaling (GO:1904262), proposed as the replacement; the kinase activity is already covered by GO:0106310 rows. The replacement crosses from the molecular-function to the biological-process aspect, so the replacement annotation takes the qualifier involved_in, not enables. Proposed replacements: negative regulation of TORC1 signaling Supporting Evidence: PMID:28057755 Gcn2 binds to TORC1 and phosphorylates Kog1, the unique regulatory subunit of TORC1, resulting in down-regulation of TORC1 kinase activity. |
| GO:0005515 protein binding | IPI PMID:11101534 Separate domains in GCN1 for binding protein kinase GCN2 and... | REMOVE | Summary: Gcn2 binds the C-terminal domain of its activator Gcn1 (P33892); the interaction is required for Gcn2 activation. Reason: The interaction is real and functionally important, but bare protein binding is uninformative and no GO MF term captures "binds its activator". Under the protein-binding policy the generic row is removed; the biology is represented by GCN2-mediated signaling and by the activator's own annotations. Removal does not dispute the interaction. Supporting Evidence: PMID:11101534 GCN2 binding to the C-terminal domain of GCN1, dependent on Arg2259, is required for high level GCN2 function in vivo. |
| GO:0005515 protein binding | IPI PMID:12628929 The path from nucleolar 90S to cytoplasmic 40S pre-ribosomes... | REMOVE | Summary: High-throughput pre-40S purification co-recovering Hrr25 (P29295). Reason: Uninformative generic protein binding from a large-scale complex purification; no functional consequence identified for Gcn2. Supporting Evidence: PMID:12628929 Our data provide an initial biochemical map of the pre-40S ribosomal subunit on its path from the nucleolus to the cytoplasm. |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: Genome-wide TAP-MS screen detecting Hrr25 (P29295) with Gcn2. Reason: Uninformative generic protein binding from a proteome-wide screen; removal does not dispute the co-purification. Supporting Evidence: PMID:16429126 Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | REMOVE | Summary: Kinase-phosphatase interaction network; Gcn2 with Npr1 (P22211). Reason: Uninformative generic protein binding from a large-scale MS network; no specific function inferred. Supporting Evidence: PMID:20489023 We identified a kinase and phosphatase interaction (KPI) network of 1844 interactions in budding yeast by mass spectrometric analysis of protein complexes. |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | REMOVE | Summary: Kinase-phosphatase interaction network; Gcn2 with Hrr25 (P29295). Reason: Uninformative generic protein binding from a large-scale MS network. Supporting Evidence: PMID:20489023 An extensive backbone of kinase-kinase interactions cross-connects the proteome and may serve to coordinate diverse cellular responses. |
| GO:0005515 protein binding | IPI PMID:21849502 Evidence that eukaryotic translation elongation factor 1A (e... | REMOVE | Summary: Gcn2 C-terminal domain binds eEF1A (P02994) directly; eEF1A inhibits Gcn2 phosphorylation of eIF2alpha. Reason: The interaction is characterized as a regulatory input on Gcn2 (eEF1A acts as an inhibitor), which is an activity of eEF1A, not of Gcn2. Generic protein binding on Gcn2 is uninformative and is removed under the protein-binding policy; the interaction itself is not disputed. Supporting Evidence: PMID:21849502 Purified GST-Gcn2-CTD and purified His(6)-eEF1A interacted with each other |
| GO:0005515 protein binding | IPI PMID:21849502 Evidence that eukaryotic translation elongation factor 1A (e... | REMOVE | Summary: Gcn2 associates with Gcn1 (P33892) in the eEF1A study. Reason: Uninformative generic protein binding; see the Gcn1 row from PMID:11101534. Supporting Evidence: PMID:21849502 Gcn1 and Gcn2 are tethered to the ribosome, and Gcn1 is directly involved in delivering uncharged tRNAs from the A-site to Gcn2 for its subsequent activation. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro protein kinase domain / ATP-binding site mapping. Reason: Gcn2 is an active protein kinase with a conserved ATP-binding lysine whose mutation abolishes activity; ATP binding is a correct, if ancillary, MF. Supporting Evidence: PMID:2188100 Substitution of a highly conserved lysine residue in the kinase domain abolished GCN2 regulatory function in vivo and its ability to autophosphorylate in vitro |
| GO:0005634 nucleus | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA to nucleus from a deep PTHR11042 node (PTN000113601) whose seeds are other kinases (WEE1/Swe1-type, PKR/PERK-type); yeast GCN2 is not among the seeds. Reason: All yeast experimental data place Gcn2 in the cytoplasm on ribosomes; its substrate eIF2 and its activators (uncharged tRNA, Gcn1 on ribosomes) are cytoplasmic. The nucleus claim derives from a broad node spanning nuclear WEE1-like kinases and is not supported for Gcn2. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000113601 SUPPORTS SOURCE BUT NOT TARGET Deep PTHR11042 node whose nuclear IBD rests on WEE1/Swe1-like and other kinases; yeast GCN2 is not a seed for this term, and all Gcn2 data place it on cytosolic ribosomes. Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:2038314}. PMID:2038314 GCN2 comigrates with ribosomal subunits and polysomes |
| GO:0005737 cytoplasm | EXP PMID:2038314 Ribosome association of GCN2 protein kinase, a translational... | MODIFY | Summary: Gcn2 cosediments with ribosomes and polysomes in cell extracts. Reason: Correct but general. The ribosome- and polysome-associated pool is cytosolic, and the gene already carries cytosol (GO:0005829) by IBA and TAS; refine to cytosol. Proposed replacements: cytosol Supporting Evidence: PMID:2038314 Centrifugation of cell extracts in sucrose gradients indicated that GCN2 comigrates with ribosomal subunits and polysomes. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MODIFY | Summary: IBA to cytoplasm from PTN000113601 (yeast GCN2 is among the seeds). Reason: Correct but general; Gcn2 acts on cytosolic ribosomes and eIF2, and cytosol (GO:0005829) is already supported by IBA and TAS rows. Refine, consistent with the EXP row. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000113601 SUPPORTS TRANSFER Cytoplasm IBD is correct for Gcn2 (yeast GCN2 is among the descendant evidence); the node stops at cytoplasm, while Gcn2 activity is in the cytosol on ribosomes. Proposed replacements: cytosol Supporting Evidence: PMID:2038314 Centrifugation of cell extracts in sucrose gradients indicated that GCN2 comigrates with ribosomal subunits and polysomes. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | MODIFY | Summary: UniProt subcellular-location mapping (Cytoplasm, experimental basis PMID:2038314). Reason: Correct but general; refine to cytosol as for the other cytoplasm rows. Proposed replacements: cytosol Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:2038314}. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA (PTN000867953, GCN2 clade) to cytosol. Reason: Gcn2 phosphorylates eIF2 on cytosolic translating ribosomes; cytosol is the correct location of its activity. Supporting Evidence: PMID:2038314 suggest that GCN2 interacts with ribosomes during the translation initiation cycle |
| GO:0005829 cytosol | TAS Reactome:R-SCE-9633467 | ACCEPT | Summary: Reactome reaction "GCN2 binds tRNA", placed in the cytosol. Reason: Consistent with the ribosome-associated cytosolic location. Supporting Evidence: Reactome:R-SCE-9633467 The histidyl-tRNA synthetase-like domain of GCN2 binds uncharged tRNA, resulting in activation of the protein kinase domain of GCN2 |
| GO:0005829 cytosol | TAS Reactome:R-SCE-9633480 | ACCEPT | Summary: Reactome reaction "GCN2 phosphorylates SUI2", placed in the cytosol. Reason: Consistent with the cytosolic location of eIF2 and the translation machinery. Supporting Evidence: Reactome:R-SCE-9633480 GCN2 phosphorylates SUI2 (eIF-2 alpha subunit) on serine-52 in response to amino acid starvation |
| GO:0005829 cytosol | TAS Reactome:R-SCE-9633750 | ACCEPT | Summary: Reactome reaction "GCN2 dimer autophosphorylates", placed in the cytosol. Reason: Consistent with the cytosolic location. Supporting Evidence: Reactome:R-SCE-9633750 After binding uncharged tRNA, the GCN2 dimer trans-autophosphorylates threonine-882 and threonine-887 |
| GO:0006446 regulation of translational initiation | IDA PMID:1739968 Phosphorylation of initiation factor 2 alpha by protein kina... | MODIFY | Summary: eIF2alpha Ser51 phosphorylation by Gcn2 mediates translational control of GCN4. Reason: Correct but general. The mechanism is precisely regulation of translational initiation by eIF2 alpha phosphorylation (GO:0010998), an is_a descendant of GO:0006446. Proposed replacements: regulation of translational initiation by eIF2 alpha phosphorylation Supporting Evidence: PMID:1739968 We show that phosphorylation of the alpha subunit of eukaryotic translation initiation factor 2 (eIF-2) by the protein kinase GCN2 mediates translational control of the yeast transcriptional activator GCN4. |
| GO:0006446 regulation of translational initiation | IDA PMID:7934812 Gene-specific translational control of the yeast GCN4 gene b... | MODIFY | Summary: Review describing GCN4 translational control by eIF2alpha phosphorylation. Reason: Correct but general; refine to GO:0010998 as for the other row. Proposed replacements: regulation of translational initiation by eIF2 alpha phosphorylation Supporting Evidence: PMID:7934812 Recent work indicates that regulation of the GCN4 gene of Saccharomyces cerevisiae by amino acid availability represents a gene-specific case of translational control by phosphorylation of eIF-2 alpha. |
| GO:0006468 protein phosphorylation | IDA PMID:10983975 Uncharged tRNA activates GCN2 by displacing the protein kina... | MODIFY | Summary: Gcn2 phosphorylates eIF2alpha and itself. Reason: Correct but general. The protein phosphorylation Gcn2 performs is eIF2alpha Ser51 phosphorylation, captured by GO:0010998 (is_a protein phosphorylation); autophosphorylation is captured by the GO:0046777 rows. Proposed replacements: regulation of translational initiation by eIF2 alpha phosphorylation Supporting Evidence: PMID:10983975 Protein kinase GCN2 regulates translation in amino acid-starved cells by phosphorylating elF2. |
| GO:0006468 protein phosphorylation | IDA PMID:1739968 Phosphorylation of initiation factor 2 alpha by protein kina... | MODIFY | Summary: Gcn2-dependent eIF2alpha phosphorylation in vivo and in vitro. Reason: Correct but general; refine to GO:0010998. Proposed replacements: regulation of translational initiation by eIF2 alpha phosphorylation Supporting Evidence: PMID:1739968 In vivo, phosphorylation of eIF-2 alpha increases in response to amino acid starvation, which is dependent on GCN2. |
| GO:0015934 large ribosomal subunit | IDA PMID:2038314 Ribosome association of GCN2 protein kinase, a translational... | KEEP AS NON CORE | Summary: Without Mg2+, nearly all Gcn2 comigrates with 60S subunits and stays bound in native gels; it is salt-extractable. Reason: Gcn2 is a peripheral, salt-sensitive ribosome-associated factor, not a ribosomal subunit component; the authors state it is not an integral ribosomal protein. The data do support Gcn2 being found on the large subunit, so the location is kept as non-core; the core location is the cytosolic ribosome and the core MF is ribosome binding. Supporting Evidence: PMID:2038314 GCN2 could be dissociated from 60S subunits by 0.5 M KCl, suggesting that it is loosely associated with ribosomes rather than being an integral ribosomal protein. |
| GO:0015935 small ribosomal subunit | IDA PMID:2038314 Ribosome association of GCN2 protein kinase, a translational... | KEEP AS NON CORE | Summary: Gcn2 accumulates on free 43S-48S particles during polysome run-off. Reason: As for the large subunit row, Gcn2 associates loosely with small-subunit-containing initiation complexes; it is not a subunit component. Kept as non-core. Supporting Evidence: PMID:2038314 Accumulation of GCN2 on free 43S-48S particles and 60S subunits occurred during polysome runoff in vitro and under conditions of reduced growth rate in vivo. |
| GO:0022626 cytosolic ribosome | IDA PMID:2038314 Ribosome association of GCN2 protein kinase, a translational... | ACCEPT | Summary: Gcn2 cosediments with ribosomes and polysomes. Reason: Ribosome association through the C-terminal domain is required for Gcn2 function; cytosolic ribosome is the site where uncharged tRNA is sensed. Supporting Evidence: PMID:2038314 The extreme carboxyl-terminal segment of GCN2 is essential for its interaction with ribosomes. These sequences are also required for the ability of GCN2 to stimulate GCN4 translation in vivo |
| GO:0031369 translation initiation factor binding | IPI PMID:21849502 Evidence that eukaryotic translation elongation factor 1A (e... | UNDECIDED | Summary: Translation initiation factor binding, WITH TIF11 (P38912, eIF1A), from a paper whose abstract describes binding of the elongation factor eEF1A to the Gcn2 C-terminus. Reason: The cached abstract names only eEF1A (an elongation factor, P02994; captured separately as a protein binding row from the same paper), not eIF1A. UniProt's SUBUNIT text also attributes this interaction to "TIF11", suggesting a possible eEF1A/eIF1A conflation, but the full text (PMC3196070) could not be retrieved to rule out an eIF1A experiment. Not removed, because the curator saw the full paper. Supporting Evidence: PMID:21849502 Using Saccharomyces cerevisiae cells expressing His(6)-eEF1A and affinity purification, we found that eEF1A co-eluted with Gcn2. |
| GO:0032057 negative regulation of translational initiation in response to stress | IBA GO_REF:0000033 | ACCEPT | Summary: IBA (PTN008315168) for negative regulation of translational initiation in response to stress. Reason: eIF2alpha phosphorylation by Gcn2 converts eIF2 into an eIF2B inhibitor and represses general initiation under starvation. Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt Converts phosphorylated eIF-2-alpha/SUI2 either to a competitive inhibitor of translation initiation factor eIF-2B, leading to a global protein synthesis repression |
| GO:0034198 cellular response to amino acid starvation | IBA GO_REF:0000033 | ACCEPT | Summary: IBA (PTN008315168) for cellular response to amino acid starvation. Reason: The defining physiological role of Gcn2, with direct yeast evidence. Supporting Evidence: PMID:7623840 We show that GCN2 phosphorylation of eIF-2, and the resulting general amino acid control pathway, is stimulated in response to starvation for each of several different amino acids, in addition to histidine limitation. |
| GO:0034198 cellular response to amino acid starvation | IDA PMID:2188100 Identification of positive-acting domains in GCN2 protein ki... | ACCEPT | Summary: Gcn2 kinase function is stimulated post-translationally in amino-acid-starved cells. Reason: Core process. Supporting Evidence: PMID:2188100 it appears that GCN2 protein kinase function is stimulated posttranslationally in amino acid-starved cells. |
| GO:0034198 cellular response to amino acid starvation | IDA PMID:3290651 Transcriptional-translational regulatory circuit in Saccharo... | ACCEPT | Summary: GCN2 is essential for translational derepression of GCN4 under amino acid starvation. Reason: Core process. Supporting Evidence: PMID:3290651 The product of the GCN2 gene is essential for translational derepression of GCN4. |
| GO:0034198 cellular response to amino acid starvation | IMP PMID:24333428 Evolutionarily conserved IMPACT impairs various stress respo... | ACCEPT | Summary: IMPACT/YIH1 study of stresses that require Gcn1-dependent Gcn2 activation. Reason: Supports the Gcn1-dependent activation of Gcn2 during amino acid depletion; consistent with the core process. Supporting Evidence: PMID:24333428 The eIF2Ξ± kinase GCN2 is activated by amino acid starvation by a mechanism involving GCN2 binding to an activator protein GCN1, along with association with uncharged tRNA that accumulates during nutrient deprivation. |
| GO:0034198 cellular response to amino acid starvation | IMP PMID:8336737 Translation of the yeast transcriptional activator GCN4 is s... | ACCEPT | Summary: GCN4 induction by purine and amino acid limitation depends on GCN2. Reason: Core process; this paper extends the response to purine starvation. Supporting Evidence: PMID:8336737 Biochemical experiments show that eIF-2 alpha is phosphorylated in response to purine starvation and that this reaction is completely dependent on GCN2. |
| GO:0035556 intracellular signal transduction | IMP PMID:8336737 Translation of the yeast transcriptional activator GCN4 is s... | MODIFY | Summary: Gcn2-dependent signaling from purine/amino acid limitation to eIF2alpha phosphorylation. Reason: Correct but general; the specific pathway is GCN2-mediated signaling (GO:0140469), an is_a descendant that the gene already carries. Proposed replacements: GCN2-mediated signaling Supporting Evidence: PMID:8336737 Biochemical experiments show that eIF-2 alpha is phosphorylated in response to purine starvation and that this reaction is completely dependent on GCN2. |
| GO:0042803 protein homodimerization activity | IDA PMID:10983975 Uncharged tRNA activates GCN2 by displacing the protein kina... | KEEP AS NON CORE | Summary: The HisRS+C-term segment binds the kinase domain in vitro; activating mutations weaken this. Reason: Gcn2 is a constitutive homodimer and dimerization is part of its activation mechanism; correct but structural/regulatory rather than the core catalytic function. Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt Homodimer; homodimerization is important for kinase activation by uncharged tRNAs |
| GO:0042803 protein homodimerization activity | IDA PMID:9566889 Dimerization by translation initiation factor 2 kinase GCN2 ... | KEEP AS NON CORE | Summary: Two-hybrid, co-IP and in vitro binding show Gcn2 dimerizes via its C-term and kinase domains. Reason: Direct evidence for homodimerization; mechanistically important but not the core activity. Supporting Evidence: PMID:9566889 These results provide in vivo and in vitro evidence that GCN2 dimerizes through self-interactions involving the C-term and PK domains. |
| GO:0043022 ribosome binding | IDA PMID:10983975 Uncharged tRNA activates GCN2 by displacing the protein kina... | ACCEPT | Summary: The C-terminal ribosome-binding segment of Gcn2 is also required for tRNA binding. Reason: Ribosome binding via the C-terminal domain is required for Gcn2 to sense uncharged tRNA and stimulate GCN4 translation; core. Supporting Evidence: PMID:10983975 Unexpectedly, the C-terminal ribosome binding segment of GCN2 (C-term) was required in addition to the HisRS domain for strong tRNA binding. |
| GO:0043022 ribosome binding | IDA PMID:21849502 Evidence that eukaryotic translation elongation factor 1A (e... | ACCEPT | Summary: Gcn2 CTD interaction with eEF1A was independent of ribosomes; study also examines Gcn2 ribosome association. Reason: Consistent with the other ribosome-binding evidence; deferring to the curator on the full-text experiment. Supporting Evidence: PMID:21849502 Gcn1 and Gcn2 are tethered to the ribosome |
| GO:0043022 ribosome binding | IDA PMID:9430731 Ribosome-binding domain of eukaryotic initiation factor-2 ki... | ACCEPT | Summary: Residues 1467-1590 independently associate with the translational machinery; DRBD lysine substitutions block ribosome association and impair translational control. Reason: Direct evidence for ribosome binding and its functional requirement; core. Supporting Evidence: PMID:9430731 Substitutions of the lysine residues conserved among DRBD sequences block association of GCN2 with ribosomes and impaired the ability of the kinase to stimulate translational control in response to amino acid limitation. |
| GO:0043023 ribosomal large subunit binding | IDA PMID:2038314 Ribosome association of GCN2 protein kinase, a translational... | ACCEPT | Summary: Gcn2 binds 60S subunits and remains bound during native gel electrophoresis. Reason: Direct evidence; consistent with ribosome binding as a core activity. Supporting Evidence: PMID:2038314 When the association of 40S and 60S subunits was prevented by omitting Mg2+ from the gradient, almost all of the GCN2 comigrated with 60S ribosomal subunits, and it remained bound to these particles during gel electrophoresis under nondenaturing conditions. |
| GO:0046777 protein autophosphorylation | IDA PMID:10983975 Uncharged tRNA activates GCN2 by displacing the protein kina... | KEEP AS NON CORE | Summary: Gcn2 autophosphorylation in vitro. Reason: Activation-loop trans-autophosphorylation (Thr882/Thr887) is part of Gcn2 activation; real but a step of the kinase's own regulation rather than its output. Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt Autophosphorylated, autophosphorylation on Thr-882 and Thr-887 increases kinase activity. |
| GO:0046777 protein autophosphorylation | IDA PMID:2188100 Identification of positive-acting domains in GCN2 protein ki... | KEEP AS NON CORE | Summary: Wild-type Gcn2 autophosphorylates; the K559 kinase-dead mutant does not. Reason: Direct evidence; non-core activation step. Supporting Evidence: PMID:2188100 abolished GCN2 regulatory function in vivo and its ability to autophosphorylate in vitro |
| GO:0071232 cellular response to histidine | IDA PMID:7621831 GCN20, a novel ATP binding cassette protein, and GCN1 reside... | MODIFY | Summary: Gcn2/Gcn1/Gcn20-dependent eIF2alpha phosphorylation and GCN4 derepression in starved cells (histidine starvation imposed by 3-aminotriazole in this system). Reason: GO:0071232 means a response to a histidine stimulus; Gcn2 responds to histidine (and other amino acid) limitation, not to histidine itself. The appropriate term is cellular response to amino acid starvation (GO:0034198), which the gene already carries. Proposed replacements: cellular response to amino acid starvation Supporting Evidence: PMID:7621831 GCN2 is a protein kinase that phosphorylates the alpha-subunit of translation initiation factor 2 (eIF-2) and thereby stimulates translation of GCN4 mRNA in amino acid-starved cells. |
| GO:0071264 positive regulation of translational initiation in response to starvation | IDA PMID:1739968 Phosphorylation of initiation factor 2 alpha by protein kina... | ACCEPT | Summary: Gcn2 phosphorylation of eIF2alpha increases GCN4 translation in starved cells. Reason: Gene-specific translational induction of GCN4 under starvation is a direct consequence of Gcn2 activity and a core output. Supporting Evidence: PMID:1739968 In vivo, phosphorylation of eIF-2 alpha increases in response to amino acid starvation, which is dependent on GCN2. |
| GO:0071264 positive regulation of translational initiation in response to starvation | IDA PMID:7623840 The histidyl-tRNA synthetase-related sequence in the eIF-2 a... | ACCEPT | Summary: Gcn2 activation by uncharged tRNA stimulates GCN4 translational expression in response to several amino acid limitations. Reason: Core output of Gcn2 signaling. Supporting Evidence: PMID:7623840 GCN2 phosphorylates eukaryotic initiation factor 2 (eIF-2), to induce the translational expression of GCN4 |
| GO:0071264 positive regulation of translational initiation in response to starvation | IMP PMID:7621831 GCN20, a novel ATP binding cassette protein, and GCN1 reside... | ACCEPT | Summary: Loss of Gcn1/Gcn20 activators impairs GCN4 translational derepression via reduced Gcn2-dependent eIF2alpha phosphorylation. Reason: Consistent with the other rows; core. Supporting Evidence: PMID:7621831 GCN2 is a protein kinase that phosphorylates the alpha-subunit of translation initiation factor 2 (eIF-2) and thereby stimulates translation of GCN4 mRNA in amino acid-starved cells. |
| GO:0106310 protein serine kinase activity | EXP PMID:10983975 Uncharged tRNA activates GCN2 by displacing the protein kina... | ACCEPT | Summary: Serine phosphorylation of eIF2alpha by Gcn2 in a tRNA-regulated assay. Reason: The Rhea-defined L-seryl-[protein] phosphorylation is directly demonstrated (eIF2alpha Ser51). Retained alongside the more specific substrate-defined GO:0004694; GO:0004694 is not an is_a descendant of this term, so it does not make the row redundant. It also covers Gcn2 phosphorylation of Kog1 (TORC1). Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) |
| GO:0106310 protein serine kinase activity | EXP PMID:17202131 Conserved intermolecular salt bridge required for activation... | ACCEPT | Summary: Salt-bridge mutants of Gcn2 lose and regain kinase activity in vitro and in yeast. Reason: Direct evidence for serine kinase activity on eIF2alpha. Supporting Evidence: PMID:17202131 Single mutations of the Asp (or Glu) and Arg residues blocked kinase function both in yeast cells and in vitro. |
| GO:0106310 protein serine kinase activity | EXP PMID:2188100 Identification of positive-acting domains in GCN2 protein ki... | ACCEPT | Summary: Gcn2 kinase activity (autophosphorylation) dependent on the catalytic lysine. Reason: Direct evidence for protein kinase activity; consistent with the other serine kinase rows. Supporting Evidence: PMID:2188100 indicating that GCN2 acts as a protein kinase in stimulating GCN4 expression |
| GO:0106310 protein serine kinase activity | EXP PMID:7623840 The histidyl-tRNA synthetase-related sequence in the eIF-2 a... | ACCEPT | Summary: Gcn2 phosphorylation of eIF2 (Ser51) stimulated by uncharged tRNA. Reason: Direct evidence. Supporting Evidence: PMID:7623840 Cells containing a defective aminoacyl-tRNA synthetase also stimulated GCN2 phosphorylation of eIF-2 in the absence of amino acid starvation |
| GO:0106310 protein serine kinase activity | EXP PMID:8798780 Histidyl-tRNA synthetase-related sequences in GCN2 protein k... | ACCEPT | Summary: In vitro phosphorylation of recombinant eIF2alpha at Ser51. Reason: Direct evidence. Supporting Evidence: PMID:8798780 Phosphorylation of the recombinant eIF-2alpha substrate was dependent on both GCN2 kinase activity and the eIF-2alpha phosphorylation site, serine 51. |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea-based electronic mapping (RHEA:17989). Reason: Agrees with the experimental rows. Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) |
| GO:0140469 GCN2-mediated signaling | IDA PMID:10983975 Uncharged tRNA activates GCN2 by displacing the protein kina... | ACCEPT | Summary: Uncharged tRNA activates Gcn2 by relieving autoinhibition. Reason: Gcn2 is the kinase that defines GCN2-mediated signaling; core process. Supporting Evidence: PMID:10983975 These results provide strong evidence that tRNA stimulates the GCN2 kinase moiety by preventing an inhibitory interaction with the bipartite tRNA binding domain. |
| GO:0140469 GCN2-mediated signaling | IDA PMID:21849502 Evidence that eukaryotic translation elongation factor 1A (e... | ACCEPT | Summary: eEF1A binding inhibits Gcn2 eIF2alpha kinase activity; relieved by starvation and uncharged tRNA. Reason: Core process. Supporting Evidence: PMID:21849502 purified eEF1A reduced the ability of Gcn2 to phosphorylate its substrate, eIF2Ξ±, but did not diminish Gcn2 autophosphorylation. |
| GO:0140469 GCN2-mediated signaling | IDA PMID:8798780 Histidyl-tRNA synthetase-related sequences in GCN2 protein k... | ACCEPT | Summary: HisRS-related sequences are needed for Gcn2 eIF2alpha kinase function. Reason: Core process. Supporting Evidence: PMID:8798780 These results indicate that the HisRS-related sequences are required for activation of GCN2 kinase function. |
| GO:0140469 GCN2-mediated signaling | IEA GO_REF:0000117 | ACCEPT | Summary: Electronic (ARBA) annotation to GCN2-mediated signaling. Reason: Agrees with abundant experimental evidence. Supporting Evidence: PMID:1739968 In vivo, phosphorylation of eIF-2 alpha increases in response to amino acid starvation, which is dependent on GCN2. |
| GO:0140469 GCN2-mediated signaling | IMP PMID:7621831 GCN20, a novel ATP binding cassette protein, and GCN1 reside... | ACCEPT | Summary: Gcn1-Gcn20 couple Gcn2 kinase activity to amino acid availability. Reason: Core process. Supporting Evidence: PMID:7621831 GCN1 and GCN20 are components of a protein complex that couples the kinase activity of GCN2 to the availability of amino acids. |
| GO:1903833 positive regulation of cellular response to amino acid starvation | IDA PMID:9430731 Ribosome-binding domain of eukaryotic initiation factor-2 ki... | ACCEPT | Summary: Ribosome binding by Gcn2 is needed for translational control in response to amino acid limitation. Reason: Gcn2 positively regulates the general amino acid control response by inducing GCN4; accepted. Supporting Evidence: PMID:9430731 These results indicate that appropriate ribosome localization of the kinase is an obligate step in the mechanism leading to translational control by GCN2. |
| GO:1903833 positive regulation of cellular response to amino acid starvation | IGI PMID:6351059 Positive regulation in the general amino acid control of Sac... | ACCEPT | Summary: Epistasis between the general-control regulators AAS1 (= GCN2), AAS2, AAS3 and TRA3 (= GCD1, SGD:S000005786, the WITH gene). Reason: Classic genetic interaction placing GCN2 (AAS1) upstream as a positive regulator that relieves GCD1 (TRA3)-mediated repression of the general amino acid control; consistent with the later mechanism (eIF2alpha phosphorylation inhibits eIF2B, of which Gcd1 is a subunit). Deferring to the curator's gene mapping. Supporting Evidence: PMID:6351059 These interactions suggest that the AAS1 and AAS2 products act indirectly to bring about derepression by disabling the repressive effect of TRA3 |
| GO:1903833 positive regulation of cellular response to amino acid starvation | IMP PMID:6351059 Positive regulation in the general amino acid control of Sac... | ACCEPT | Summary: aas mutants cannot derepress the general control. Reason: Mutant evidence that GCN2 is a positive regulator of the response. Supporting Evidence: PMID:6351059 mutations in AAS genes lead to the inability to derepress |
| GO:1903833 positive regulation of cellular response to amino acid starvation | IMP PMID:7623840 The histidyl-tRNA synthetase-related sequence in the eIF-2 a... | ACCEPT | Summary: HisRS-domain mutants abolish Gcn2 activation and the general amino acid control response. Reason: Mutant evidence; consistent with core role. Supporting Evidence: PMID:7623840 Mutations in the motif 2 sequence conserved among class II synthetases, including histidyl-tRNA synthetases, impair the ability of this synthetase-related domain to bind tRNA and abolish GCN2 phosphorylation of eIF-2 required to stimulate the general amino acid control response. |
| GO:1990611 regulation of cytoplasmic translational initiation in response to stress | IEA GO_REF:0000117 | ACCEPT | Summary: Electronic (ARBA) annotation to regulation of cytoplasmic translational initiation in response to stress. Reason: Accurate description of Gcn2's role. Supporting Evidence: file:yeast/GCN2/GCN2-uniprot.txt Converts phosphorylated eIF-2-alpha/SUI2 either to a competitive inhibitor of translation initiation factor eIF-2B, leading to a global protein synthesis repression |
| GO:1990611 regulation of cytoplasmic translational initiation in response to stress | IMP PMID:24333428 Evolutionarily conserved IMPACT impairs various stress respo... | ACCEPT | Summary: Gcn2 activation under multiple stresses (acetic acid, NaCl, H2O2, benomyl) requires Gcn1 and is inhibited by YIH1/IMPACT. Reason: Supports Gcn2-dependent translational control under various stresses. Supporting Evidence: PMID:24333428 overexpression of IMPACT in yeast cells inhibited growth under all stress conditions that require GCN2 and GCN1 for cell survival, including exposure to acetic acid, high levels of NaCl, HβOβ or benomyl. |
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Download this section (compressed HTML)Q: PMID:21849502 describes binding of the elongation factor eEF1A (TEF1/TEF2) to the Gcn2 C-terminus, yet GOA carries a translation initiation factor binding row WITH TIF11 (eIF1A) from this paper and UniProt's SUBUNIT note names TIF11. Was eIF1A tested, or is this an eEF1A/eIF1A conflation?
Q: Gcn2 phosphorylation of Kog1 down-regulates TORC1 (PMID:28057755). Should this be captured as protein serine kinase activity with negative regulation of TORC1 signaling (GO:1904262), rather than protein kinase inhibitor activity?
Experiment: Compare G1/S delay after MMS in gcn2-deleted cells, cells carrying non-phosphorylatable eIF2alpha S51A, and S51D phosphomimetic cells lacking Gcn2, and test whether GCN4 deletion phenocopies the gcn2 defect.
Hypothesis: The Gcn2 contribution to the G1/S DNA-damage checkpoint acts through eIF2alpha phosphorylation rather than through a separate checkpoint substrate.
Protein kinase; phosphorylates the alpha-subunit of translation initiation factor eIF2 (Sui2p) in response to starvation; activated by uncharged tRNAs and the Gcn1p-Gcn20p complex; contributes to DNA damage checkpoint control
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