GCN1 (stalled ribosome sensor GCN1, formerly GCN1L1) is a very large cytoplasmic HEAT-repeat/alpha-solenoid protein that binds directly to ribosomes and acts as a sentinel for stalled and collided ribosomes. Through its RWD-binding domain it engages RWD-domain proteins and serves two intertwined ribosome-surveillance functions. First, GCN1 activates the eIF2alpha kinase GCN2 (EIF2AK4) on translating ribosomes, stimulating GCN2 to phosphorylate eIF2alpha (EIF2S1) and thereby triggering the integrated stress response and the cellular response to amino-acid starvation (the GCN2-mediated signaling axis conserved from yeast GCN1/GCN20). Second, GCN1 is the collision sensor of the RNF14-RNF25 translation quality-control pathway, where it is required for ubiquitination and degradation of translation factors (eEF1A/eEF1A1, eRF1/ETF1) and ribosomal proteins on stalled ribosomes, including resolution of formaldehyde-induced mRNA RNA-protein crosslinks. GCN1 binding by IMPACT antagonizes GCN2 activation. GCN1 is ribosome/polysome-associated in the cytosol.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006417 regulation of translation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Broad phylogenetically inferred process term. GCN1's specific roles are activation of the GCN2/ISR pathway and collided-ribosome quality control; these down-regulate translation, but the broad term is non-specific. Reason: Correct in direction but too general; the informative core roles (GCN2 activation/ISR and RQC) are captured by more specific terms. Supporting Evidence: file:human/GCN1/GCN1-goa.tsv GO:0006417 regulation of translation biological_process ECO:0000318 IBA |
| GO:0019887 protein kinase regulator activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: GCN1 regulates (activates) the protein kinase GCN2/EIF2AK4. This is a core molecular function, though the more specific protein serine/threonine kinase activator activity term is preferable. Reason: Accurate but less specific than the protein serine/threonine kinase activator activity term that more precisely captures GCN1's activation of GCN2; retained as a valid parent. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt stimulates EIF2AK4/GCN2 kinase activity, leading to phosphorylation of eukaryotic translation initiation factor 2 |
| GO:0034198 cellular response to amino acid starvation | IBA GO_REF:0000033 | ACCEPT | Summary: GCN1 mediates activation of GCN2 in response to amino-acid starvation, a conserved role (yeast GCN1/GCN20 -> GCN2 -> eIF2alpha -> GCN4/ATF4). This is a core biological process for GCN1. Reason: Well-supported, conserved core role of GCN1 in the amino-acid starvation response via GCN2 activation. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt positive activator of the integrated stress response (ISR) by mediating activation of EIF2AK4/GCN2 in response to amino acid starvation |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: GCN1 acts in the cytosol, associated with ribosomes/polysomes. Phylogenetically inferred and experimentally supported. Reason: Correct site of action for this cytosolic ribosome-associated sensor. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation of cytoplasmic localization, consistent with the documented cytoplasmic/ribosome-associated location of GCN1. Reason: Correct compartment, corroborated by experimental and similarity evidence. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0005515 protein binding | IPI PMID:17314511 Large-scale identification of c-MYC-associated proteins usin... | KEEP AS NON CORE | Summary: c-MYC interactome (TAP/MudPIT) screen capturing a GCN1-MYC (P01106) interaction. GCN1 is a very large, abundant ribosome-associated protein; this isolated high-throughput interaction does not inform its core function. Reason: Bare protein binding from a single large-scale affinity screen with a partner (MYC) unrelated to GCN1's ribosome-surveillance function; uninformative and not core. Supporting Evidence: file:human/GCN1/GCN1-goa.tsv GO:0005515 protein binding molecular_function ECO:0000353 IPI PMID:17314511 UniProtKB:P01106 |
| GO:0005515 protein binding | IPI PMID:20936779 A human MAP kinase interactome. | KEEP AS NON CORE | Summary: Human MAP kinase interactome screen capturing a GCN1-MYC (P01106) interaction. Isolated high-throughput interaction unrelated to GCN1's core function. Reason: Bare protein binding from a high-throughput interactome with an unrelated partner; uninformative and not core. Supporting Evidence: file:human/GCN1/GCN1-goa.tsv GO:0005515 protein binding molecular_function ECO:0000353 IPI PMID:20936779 UniProtKB:P01106 |
| GO:0005515 protein binding | IPI PMID:38884001 Mapping adipocyte interactome networks by HaloTag-enrichment... | KEEP AS NON CORE | Summary: Adipocyte HaloTag-enrichment mass-spectrometry interactome capturing a GCN1-MYC (P01106) interaction. Isolated high-throughput interaction unrelated to GCN1's core function. Reason: Bare protein binding from a high-throughput proteomic screen with an unrelated partner; uninformative and not core. Supporting Evidence: file:human/GCN1/GCN1-goa.tsv GO:0005515 protein binding molecular_function ECO:0000353 IPI PMID:38884001 UniProtKB:P01106 |
| GO:0034198 cellular response to amino acid starvation | IEA GO_REF:0000107 | ACCEPT | Summary: Ortholog-based electronic annotation of the amino-acid starvation response, consistent with GCN1's conserved role in GCN2 activation. Reason: Correct core biological process, corroborated by experimental/ISS evidence. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt positive activator of the integrated stress response (ISR) by mediating activation of EIF2AK4/GCN2 in response to amino acid starvation |
| GO:0043539 protein serine/threonine kinase activator activity | IEA GO_REF:0000107 | ACCEPT | Summary: GCN1 activates the serine/threonine kinase GCN2/EIF2AK4 on translating ribosomes, stimulating eIF2alpha phosphorylation. This is a core molecular function. Reason: Precisely captures GCN1's core activity as an activator of the GCN2 protein serine/threonine kinase. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt stimulates EIF2AK4/GCN2 kinase activity, leading to phosphorylation of eukaryotic translation initiation factor 2 |
| GO:0140469 GCN2-mediated signaling | IEA GO_REF:0000107 | ACCEPT | Summary: GCN1 is upstream activator of GCN2-mediated signaling. Core biological process capturing the ISR-activation role. Reason: Directly reflects GCN1's role in stimulating GCN2 signaling; core process. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt Interaction with EIF2AK4/GCN2 on translating ribosomes stimulates EIF2AK4/GCN2 kinase activity |
| GO:0005829 cytosol | IDA GO_REF:0000052 | ACCEPT | Summary: Direct immunofluorescence (HPA) evidence for cytosolic localization, consistent with GCN1's ribosome-associated cytosolic location. Reason: IDA-supported cytosolic localization matching the documented site of action. Supporting Evidence: file:human/GCN1/GCN1-goa.tsv GO:0005829 cytosol cellular_component ECO:0000314 IDA GO_REF:0000052 |
| GO:0022626 cytosolic ribosome | IDA PMID:36638793 An E3 ligase network engages GCN1 to promote the degradation... | ACCEPT | Summary: GCN1 is active on the cytosolic ribosome, where it senses collided ribosomes and engages RNF14. Direct experimental evidence. Reason: Core cellular component/site of action; GCN1 binds and acts on cytosolic ribosomes. Supporting Evidence: PMID:36638793 GCN1 is a conserved ribosome-associated scaffolding protein that binds the RWD domain of the integrated stress response kinase, GCN2 |
| GO:0170011 stalled ribosome sensor activity | IDA PMID:36638793 An E3 ligase network engages GCN1 to promote the degradation... | ACCEPT | Summary: GCN1 directly senses stalled/collided ribosomes (occluded A site) and recruits RNF14, triggering degradation of translation factors. This is the core molecular function of GCN1. Reason: Directly demonstrated core MF; GCN1 is the ribosome collision sensor of the RNF14-RNF25 quality-control pathway. Supporting Evidence: PMID:36638793 The ribosome collision sensor GCN1 plays an file:human/GCN1/GCN1-uniprot.txt acts as a sentinel for colliding ribosomes |
| GO:0005737 cytoplasm | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity-based annotation of cytoplasmic localization, consistent with experimental evidence. Reason: Correct compartment, corroborated by IDA evidence. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0160127 protein-RNA covalent cross-linking repair | IDA PMID:37951215 K6-linked ubiquitylation marks formaldehyde-induced RNA-prot... | ACCEPT | Summary: GCN1 is required for translation-coupled resolution of formaldehyde-induced mRNA RNA-protein crosslinks that stall ribosomes (RNF14/RNF25 pathway). A specific RQC-adjacent biological process. Reason: GCN1's collision-sensing role is required for resolving ribosome stalls at RNA-protein crosslinks; supported by the companion RNF14 crosslink-resolution studies. Supporting Evidence: PMID:37951216 which also requires the ribosome collision sensor GCN1 file:human/GCN1/GCN1-goa.tsv GO:0160127 protein-RNA covalent cross-linking repair biological_process ECO:0000314 IDA PMID:37951215 |
| GO:0072344 rescue of stalled cytosolic ribosome | IDA PMID:37651229 Drug-induced eRF1 degradation promotes readthrough and revea... | ACCEPT | Summary: GCN1 functions in a branch of ribosome-associated quality control that rescues stalled ribosomes via RNF14/RNF25-mediated degradation of A-site-blocking factors (here eRF1). Core RQC biological process. Reason: Directly supported role of GCN1 in stalled-ribosome rescue through the RNF14/RNF25 pathway. Supporting Evidence: PMID:37651229 activating a branch of the ribosome-associated quality control network, which involves the translational stress sensor GCN1 and the catalytic activity of the E3 ubiquitin ligases RNF14 and RNF25 |
| GO:0072344 rescue of stalled cytosolic ribosome | IDA PMID:37951215 K6-linked ubiquitylation marks formaldehyde-induced RNA-prot... | ACCEPT | Summary: GCN1 is required for resolution of ribosomes stalled at formaldehyde-induced RNA-protein crosslinks (RNF14 pathway). Core RQC biological process. Reason: Supported by the RNF14 crosslink-resolution studies that require the collision sensor GCN1. Supporting Evidence: PMID:37951216 which also requires the ribosome collision sensor GCN1 |
| GO:0072344 rescue of stalled cytosolic ribosome | IDA PMID:37951216 RNF14-dependent atypical ubiquitylation promotes translation... | ACCEPT | Summary: RNF14-dependent atypical ubiquitylation promotes translation-coupled resolution of RNA-protein crosslinks and requires the ribosome collision sensor GCN1. Core RQC biological process. Reason: Directly supported; GCN1 is required for RNF14/RNF25-mediated resolution of stalled ribosomes. Supporting Evidence: PMID:37951216 which also requires the ribosome collision sensor GCN1 |
| GO:0170011 stalled ribosome sensor activity | IDA PMID:37651229 Drug-induced eRF1 degradation promotes readthrough and revea... | ACCEPT | Summary: GCN1 senses stalled ribosomes (here induced by eRF1 depletion/readthrough) to engage the RNF14/RNF25 RQC branch. Core molecular function. Reason: Directly demonstrated core sensor MF in a second independent stalling context. Supporting Evidence: PMID:37651229 activating a branch of the ribosome-associated quality control network, which involves the translational stress sensor GCN1 and the catalytic activity of the E3 ubiquitin ligases RNF14 and RNF25 |
| GO:0170011 stalled ribosome sensor activity | IDA PMID:37951215 K6-linked ubiquitylation marks formaldehyde-induced RNA-prot... | ACCEPT | Summary: GCN1 senses ribosomes stalled at formaldehyde-induced RNA-protein crosslinks. Core molecular function. Reason: Directly supported core sensor MF in the RNA-protein crosslink stalling context. Supporting Evidence: PMID:37951216 which also requires the ribosome collision sensor GCN1 |
| GO:0170011 stalled ribosome sensor activity | IDA PMID:37951216 RNF14-dependent atypical ubiquitylation promotes translation... | ACCEPT | Summary: GCN1 senses stalled/collided ribosomes in the RNF14-dependent crosslink-resolution pathway. Core molecular function. Reason: Directly supported core sensor MF. Supporting Evidence: PMID:37951216 which also requires the ribosome collision sensor GCN1 |
| GO:0043539 protein serine/threonine kinase activator activity | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity-based annotation of GCN2 (serine/threonine kinase) activator activity, consistent with the conserved GCN1->GCN2 activation role. Reason: Core MF, corroborated by experimental and ortholog evidence. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt stimulates EIF2AK4/GCN2 kinase activity, leading to phosphorylation of eukaryotic translation initiation factor 2 |
| GO:0060090 molecular adaptor activity | IDA PMID:36638793 An E3 ligase network engages GCN1 to promote the degradation... | ACCEPT | Summary: GCN1 acts as a ribosome-associated scaffold/adaptor that, via its RWD-binding domain, brings RWD-domain partners (GCN2, RNF14, IMPACT) to stalled ribosomes. A reasonable molecular-function description of its scaffolding role. Reason: GCN1 is described as a scaffolding protein that recruits RWD-domain effectors to the ribosome; adaptor activity captures this bridging function. Supporting Evidence: PMID:36638793 GCN1 is a conserved ribosome-associated scaffolding protein that binds the RWD domain of the integrated stress response kinase, GCN2 |
| GO:0072344 rescue of stalled cytosolic ribosome | IDA PMID:36638793 An E3 ligase network engages GCN1 to promote the degradation... | ACCEPT | Summary: GCN1 senses stalled ribosomes and recruits RNF14 to ubiquitinate and degrade A-site-blocking translation factors (eEF1A), a stalled-ribosome rescue process. Core RQC biological process. Reason: Directly demonstrated; GCN1 is essential for RNF14/RNF25-mediated rescue of stalled ribosomes. Supporting Evidence: PMID:36638793 interacts with RNF14 and is also essential for eEF1A degradation |
| GO:0140469 GCN2-mediated signaling | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity-based annotation of GCN1's role in GCN2-mediated signaling, consistent with experimental evidence. Reason: Core process; GCN1 is the upstream activator of GCN2 signaling. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt Interaction with EIF2AK4/GCN2 on translating ribosomes stimulates EIF2AK4/GCN2 kinase activity |
| GO:0045296 cadherin binding | HDA PMID:25468996 E-cadherin interactome complexity and robustness resolved by... | MARK AS OVER ANNOTATED | Summary: High-throughput quantitative proteomics of the E-cadherin interactome capturing GCN1. GCN1 is a very large, abundant ribosome-associated protein; this is a non-specific proximity/affinity capture, not a genuine cadherin-binding function. Reason: HDA proteomic capture inconsistent with GCN1's known cytosolic ribosome-surveillance function; likely a non-specific co-purification. Supporting Evidence: file:human/GCN1/GCN1-goa.tsv GO:0045296 cadherin binding molecular_function ECO:0007005 HDA PMID:25468996 |
| GO:0016020 membrane | HDA PMID:19946888 Defining the membrane proteome of NK cells. | MARK AS OVER ANNOTATED | Summary: High-throughput NK-cell membrane proteome capture. GCN1 is a cytosolic ribosome-associated protein; membrane localization is inconsistent with its established biology. Reason: HDA membrane-proteome capture conflicts with the well-documented cytosolic/ribosomal localization of GCN1; likely a contaminant in the membrane fraction. Supporting Evidence: file:human/GCN1/GCN1-goa.tsv GO:0016020 membrane cellular_component ECO:0007005 HDA PMID:19946888 |
| GO:0003723 RNA binding | HDA PMID:22681889 The mRNA-bound proteome and its global occupancy profile on ... | KEEP AS NON CORE | Summary: mRNA-interactome capture identifying GCN1 as an RNA-associated protein. GCN1 associates with ribosomes/rRNA and senses mRNA-bound stalled ribosomes, so some RNA association is expected, but the bare RNA binding term is non-specific and not the informative core function. Reason: Plausible given ribosome/mRNA association, but uninformative relative to GCN1's core sensor/scaffold and kinase-activator roles. Supporting Evidence: file:human/GCN1/GCN1-goa.tsv GO:0003723 RNA binding molecular_function ECO:0007005 HDA PMID:22681889 |
| GO:0005737 cytoplasm | NAS PMID:9234705 Evidence that GCN1 and GCN20, translational regulators of GC... | ACCEPT | Summary: Non-traceable author statement of cytoplasmic localization from the classic yeast GCN1/GCN20 study, consistent with the documented cytoplasmic location. Reason: Consistent with experimental and similarity evidence for cytoplasmic localization. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0005840 ribosome | NAS PMID:9234705 Evidence that GCN1 and GCN20, translational regulators of GC... | ACCEPT | Summary: Author statement that GCN1 (with GCN20) co-sediments with polysomes/80S ribosomes and functions on elongating ribosomes. Consistent with GCN1's ribosome-associated role. Reason: Correct ribosome-associated localization, consistent with the cytosolic ribosome IDA annotation and GCN1's mechanism. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt Associates with ribosomes |
| GO:0008135 translation factor activity, RNA binding | NAS PMID:9234705 Evidence that GCN1 and GCN20, translational regulators of GC... | MARK AS OVER ANNOTATED | Summary: Outdated framing of GCN1 as a translation factor from the 1997 yeast study. GCN1 is now understood as a ribosome collision sensor and scaffold/activator of GCN2, not a canonical translation factor. Reason: GCN1's molecular function is better captured by stalled ribosome sensor activity and kinase activator activity; the generic translation-factor MF is a legacy over-annotation. Supporting Evidence: file:human/GCN1/GCN1-uniprot.txt acts as a sentinel for colliding ribosomes |
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Download this section (compressed HTML)Q: What structural features distinguish GCN1's recognition of collided ribosomes that activate GCN2/ISR versus those that engage the RNF14-RNF25 degradation branch?
Q: How is the choice between GCN2-mediated ISR signaling and RNF14/RNF25-mediated factor degradation coordinated on the same stalled-ribosome substrate, and what determines the balance?
Q: Does IMPACT-mediated antagonism of GCN1-GCN2 binding also modulate the RNF14 quality-control branch?
Experiment: Cryo-EM of GCN1 bound to collided (disome) ribosomes with and without GCN2, RNF14 or IMPACT to define how the HEAT-repeat solenoid and RWD-binding domain discriminate substrates and effectors.
Experiment: Degron/ubiquitination kinetics (eEF1A, eRF1) on stalled-ribosome reporters in GCN1-knockout versus wild-type cells to quantify GCN1's requirement across distinct stalling stimuli (poly(A), ternatin-4, formaldehyde RPCs, eRF1 depletion).
Experiment: Phospho-eIF2alpha and ATF4 reporter assays in GCN1-knockout cells under amino-acid starvation versus collision stress to dissect the GCN2-activation versus RQC functions of GCN1.
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