{"gene":"SMG9","run_date":"2026-06-10T07:46:35","timeline":{"discoveries":[{"year":2009,"finding":"SMG-9 (together with SMG-8) was identified as a novel subunit of the SMG-1 kinase complex; SMG-8 and SMG-9 suppress SMG-1 kinase activity in the isolated SMG-1 complex and are involved in NMD in both mammals and nematodes. SMG-8 recruits SMG-1 to the mRNA surveillance complex.","method":"Co-immunoprecipitation, functional RNAi knockdown in mammals and C. elegans, biochemical fractionation","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, multiple orthogonal methods (kinase assays, RNAi in two organisms), replicated across labs subsequently","pmids":["19417104"],"is_preprint":false},{"year":2010,"finding":"SMG-9 comprises an N-terminal intrinsically disordered region (IDR, ~180 residues) followed by a well-folded C-terminal domain; both domains are required for SMG-1 binding and SMG1C complex integrity, whereas the C-terminus alone is sufficient to interact with SMG-8. SMG-9 also forms SMG-9:SMG-9 homo-oligomers and SMG-8:SMG-9 complexes that are distinct from SMG1C.","method":"Biochemical domain-deletion mapping, co-immunoprecipitation, biophysical characterization (SEC, limited proteolysis), electron microscopy","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal biochemical methods (deletion mapping, Co-IP, EM), single lab but comprehensive domain dissection","pmids":["20817927"],"is_preprint":false},{"year":2015,"finding":"Cryo-EM of the SMG-1-8-9-UPF1 complex revealed that UPF1 is recruited to both the SMG-1 kinase domain and C-terminal insertion domain, inducing opening of the head domain to expose the active site. SMG-8 and SMG-9 interact with the SMG-1 C-insertion domain, promoting high-affinity UPF1 binding while decelerating SMG-1 kinase activity and enhancing stringency of phosphorylation site selection. UPF2 binding destabilizes the SMG-1-8-9-UPF1 complex, promoting substrate release.","method":"Electron cryo-microscopy (cryo-EM) of SMG-1-8-9-UPF1 complex, biochemical binding assays, kinase activity assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structural analysis combined with biochemical kinase assays, single lab but multiple orthogonal methods","pmids":["26130714"],"is_preprint":false},{"year":2017,"finding":"Crystal structure (2.5 Å) of the SMG8-SMG9 core complex from C. elegans revealed a G-domain heterodimer with architectural similarity to dynamin-like GTPases (Atlastin, GBP1). Nucleotide binding occurs at the G domain of SMG9 but not of SMG8. The heterodimer forms in the absence of nucleotides, with interactions conserved from worms to humans.","method":"X-ray crystallography (2.5 Å), nucleotide-binding assays, fitting into EM densities of human SMG1-SMG8-SMG9","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — atomic-resolution crystal structure with functional nucleotide-binding validation, single lab","pmids":["28389433"],"is_preprint":false},{"year":2019,"finding":"Cryo-EM structure (3.4 Å) of the human SMG1-SMG8-SMG9 complex showed that SMG8 contains a C-terminal kinase inhibitory domain (KID) that covers the catalytic pocket of SMG1. Structural analysis suggested GTP hydrolysis by SMG9 would cause a conformational change moving the KID away from the inhibitory position to restore SMG1 kinase activity.","method":"Cryo-EM (3.4 Å and 3.6 Å resolution), biochemical kinase inhibition assays","journal":"Cell research","confidence":"High","confidence_rationale":"Tier 1 / Strong — near-atomic cryo-EM structures independently determined by two groups (PMIDs 31729466 and 31792449) in the same year","pmids":["31729466"],"is_preprint":false},{"year":2019,"finding":"Cryo-EM structure (3.45 Å) of human SMG1-SMG8-SMG9 combined with MS analysis revealed the presence of inositol hexaphosphate (InsP6) bound in the SMG1 kinase; the InsP6-binding site is required for optimal in vitro phosphorylation of SMG1 substrates.","method":"Cryo-EM (3.45 Å), mass spectrometry, in vitro kinase activity assays with InsP6-binding site mutants","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution structure plus MS plus functional mutagenesis, replicated structural finding across two contemporaneous studies","pmids":["31792449"],"is_preprint":false},{"year":2011,"finding":"SMG-9 is tyrosine-phosphorylated at Tyr-41; phosphorylation at this site regulates binding of SMG-9 to IQGAP1, an actin cytoskeleton modifier. SMG-9 co-localizes with IQGAP1 at sites of actin enrichment in non-stimulated cells but not in EGF-stimulated cells. EGF stimulation increases the ability of SMG-9 to bind SMG-8.","method":"Co-immunoprecipitation, phospho-site mutagenesis (Tyr-41), immunofluorescence co-localization, EGF stimulation assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-IP with mutagenesis and co-localization, single lab, limited orthogonal validation","pmids":["21640080"],"is_preprint":false},{"year":2021,"finding":"SMG9 directly binds GPX4 and promotes its degradation in response to the GPX4 inhibitor RSL3 (but not erastin). Genetic inhibition of SMG9 increases GPX4 accumulation specifically in mitochondria, preventing mitochondrial oxidative damage and conferring ferroptosis resistance. This function is independent of SMG9's role in NMD.","method":"RNAi screen, co-immunoprecipitation (SMG9-GPX4 direct binding), siRNA knockdown, subcellular fractionation (mitochondrial GPX4 accumulation), xenograft mouse models","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP demonstrating direct binding plus functional loss-of-function phenotype in vitro and in vivo, single lab, limited mechanistic detail on degradation mechanism","pmids":["34146907"],"is_preprint":false},{"year":2022,"finding":"Loss-of-function mutations in SMG9 (or SMG8) cause ATR inhibitor resistance through an SMG1-mediated mechanism. SMG8/9-deficient cells showed reduced ATRi-induced transcription/replication conflicts (TRCs) and lacked characteristic ATRi-induced DNA damage signaling changes (ATM/CHK2, γH2AX, phospho-RPA, 53BP1), establishing SMG8/SMG9/SMG1 pathway involvement in the cellular response to replication stress.","method":"Genome-wide CRISPR-Cas9 resistance screen, loss-of-function genetic validation, cell cycle analysis, DNA damage marker immunofluorescence, TRC measurement assays","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide CRISPR screen followed by genetic validation and multiple phenotypic readouts, single lab","pmids":["36273494"],"is_preprint":false},{"year":2026,"finding":"Complete deletion of SMG9 (or SMG8) in human cells caused only modest NMD impairment with moderately increased UPF1 phosphorylation. Deletion of the SMG8 kinase inhibitory domain (KID) alone did not affect UPF1 phosphorylation or NMD efficiency, demonstrating the KID is dispensable in vivo. However, SMG9-deficient (and SMG8-deficient) cells showed pronounced hypersensitivity to partial pharmacological SMG1 inhibition, establishing SMG8 and SMG9 as nonessential modulators that safeguard NMD efficiency and perturbation tolerance.","method":"CRISPR-Cas9 gene deletion, pharmacological SMG1 inhibition, RNA-seq transcriptome-wide NMD target analysis, UPF1 phosphorylation western blot, multiple human cell lines","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean genetic KO combined with pharmacological perturbation and transcriptome-wide readout across multiple cell lines, comprehensive dissection","pmids":["41830328"],"is_preprint":false}],"current_model":"SMG9 is a regulatory subunit of the SMG1C kinase complex (SMG1-SMG8-SMG9) that forms a G-domain heterodimer with SMG8; SMG9's GTPase domain promotes conformational changes that relieve SMG8-mediated inhibition of SMG1's catalytic pocket, while together SMG8 and SMG9 modulate UPF1 substrate recruitment and phosphorylation stringency to safeguard nonsense-mediated mRNA decay efficiency. Beyond NMD, SMG9 is tyrosine-phosphorylated at Tyr-41 to regulate IQGAP1 binding and actin cytoskeleton association, directly binds and promotes mitochondrial GPX4 degradation to drive ferroptosis, and its loss confers ATR inhibitor resistance via an SMG1-dependent mechanism."},"narrative":{"mechanistic_narrative":"SMG9 is a regulatory subunit of the SMG1 kinase complex (SMG1C) that safeguards the efficiency of nonsense-mediated mRNA decay (NMD) [PMID:19417104, PMID:41830328]. Together with SMG8, SMG9 was identified as a component of the SMG1 complex that suppresses SMG1 kinase activity and is required for NMD in mammals and nematodes [PMID:19417104]. SMG9 consists of an N-terminal intrinsically disordered region and a folded C-terminal domain, both required for SMG1 binding and SMG1C integrity, while its C-terminus mediates interaction with SMG8 [PMID:20817927]. The SMG8-SMG9 pair forms a G-domain heterodimer architecturally related to dynamin-like GTPases, with nucleotide binding occurring at the SMG9 G domain but not SMG8 [PMID:28389433]. Within SMG1C, SMG8 carries a C-terminal kinase inhibitory domain (KID) that occludes the SMG1 catalytic pocket, and structural analysis indicates GTP hydrolysis by SMG9 repositions the KID to restore kinase activity [PMID:31729466]. During substrate engagement, SMG8 and SMG9 promote high-affinity UPF1 binding while decelerating SMG1 and enhancing the stringency of phosphorylation-site selection [PMID:26130714]. Genetic deletion of SMG9 causes only modest NMD impairment with moderately elevated UPF1 phosphorylation, establishing SMG8 and SMG9 as nonessential modulators that buffer NMD against perturbation, since SMG9-deficient cells are hypersensitive to partial SMG1 inhibition [PMID:41830328]. Beyond NMD, SMG9 is tyrosine-phosphorylated at Tyr-41 to regulate IQGAP1 binding and actin-cytoskeleton association [PMID:21640080], directly binds GPX4 to promote its mitochondrial degradation and drive ferroptosis [PMID:34146907], and its loss confers ATR-inhibitor resistance through an SMG1-dependent effect on replication stress signaling [PMID:36273494].","teleology":[{"year":2009,"claim":"Established SMG9 as a bona fide subunit of the SMG1 kinase complex and a functional NMD factor, defining its core biological context.","evidence":"Co-IP, RNAi knockdown in mammals and C. elegans, biochemical fractionation","pmids":["19417104"],"confidence":"High","gaps":["Molecular basis of kinase suppression not resolved","Domain requirements for complex assembly undefined"]},{"year":2010,"claim":"Resolved SMG9's domain organization, showing both its IDR and folded C-terminus are required for SMG1C integrity while the C-terminus alone binds SMG8.","evidence":"Domain-deletion mapping, Co-IP, SEC, limited proteolysis, EM","pmids":["20817927"],"confidence":"High","gaps":["Functional role of SMG9 homo-oligomers and SMG8:SMG9 sub-complexes unknown","No atomic structure of the interfaces"]},{"year":2015,"claim":"Defined how SMG8/SMG9 shape catalysis by showing they promote high-affinity UPF1 recruitment while decelerating SMG1 and sharpening phosphosite selection, with UPF2 triggering substrate release.","evidence":"Cryo-EM of SMG1-8-9-UPF1, binding and kinase assays","pmids":["26130714"],"confidence":"High","gaps":["SMG9-specific contributions not separated from SMG8","Conformational dynamics not captured at high resolution"]},{"year":2017,"claim":"Revealed the SMG8-SMG9 core as a G-domain heterodimer resembling dynamin-like GTPases, localizing nucleotide binding to SMG9, providing a structural basis for a GTPase-driven regulatory switch.","evidence":"X-ray crystallography (2.5 Å) of C. elegans SMG8-SMG9, nucleotide-binding assays, EM fitting","pmids":["28389433"],"confidence":"High","gaps":["GTP hydrolysis activity and turnover not measured","Coupling of nucleotide state to kinase regulation untested"]},{"year":2019,"claim":"Connected SMG9's GTPase domain to kinase control by showing SMG8's KID occludes the SMG1 catalytic pocket and that SMG9-driven conformational change would relieve this inhibition; an InsP6 cofactor supports optimal substrate phosphorylation.","evidence":"Cryo-EM (3.4–3.45 Å) of human SMG1-8-9, MS, kinase assays with InsP6-site mutants","pmids":["31729466","31792449"],"confidence":"High","gaps":["Direct demonstration that SMG9 GTP hydrolysis triggers KID release in vivo absent","Timing of the switch during NMD undefined"]},{"year":2011,"claim":"Identified a non-NMD activity in which Tyr-41 phosphorylation of SMG9 governs binding to the actin modifier IQGAP1, implicating SMG9 in cytoskeletal signaling.","evidence":"Co-IP, Tyr-41 phospho-mutagenesis, immunofluorescence, EGF stimulation","pmids":["21640080"],"confidence":"Medium","gaps":["Kinase responsible for Tyr-41 phosphorylation unknown","Functional consequence for actin dynamics not established","Single lab, limited orthogonal validation"]},{"year":2021,"claim":"Showed an NMD-independent role: SMG9 directly binds GPX4 and promotes its mitochondrial degradation, sensitizing cells to RSL3-induced ferroptosis.","evidence":"RNAi screen, Co-IP, siRNA knockdown, subcellular fractionation, xenografts","pmids":["34146907"],"confidence":"Medium","gaps":["Mechanism of GPX4 degradation not defined","How SMG9 distinguishes mitochondrial GPX4 pools unclear","Single lab"]},{"year":2022,"claim":"Linked SMG9 to replication stress responses by showing its loss causes ATR-inhibitor resistance via an SMG1-mediated reduction in transcription-replication conflicts and DNA damage signaling.","evidence":"Genome-wide CRISPR resistance screen, genetic validation, DNA damage marker IF, TRC assays","pmids":["36273494"],"confidence":"Medium","gaps":["Molecular target of SMG1 in this pathway unidentified","Whether the role requires NMD vs. a direct activity unresolved","Single lab"]},{"year":2026,"claim":"Reframed SMG9 (and SMG8) as nonessential NMD modulators by showing their deletion only modestly impairs NMD but sensitizes cells to partial SMG1 inhibition, and that the SMG8 KID is dispensable in vivo.","evidence":"CRISPR KO, pharmacological SMG1 inhibition, RNA-seq, UPF1 phospho-blot across cell lines","pmids":["41830328"],"confidence":"High","gaps":["In vivo trigger and timing of the GTPase switch still undefined","Reconciliation of dispensable KID with structural inhibition model incomplete"]},{"year":null,"claim":"Whether and how SMG9 GTP hydrolysis is catalytically coupled to relief of SMG8-mediated kinase inhibition during a physiological NMD cycle remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No measurement of SMG9 GTPase turnover within active SMG1C in cells","Mechanistic basis of NMD-independent functions (ferroptosis, replication stress, cytoskeleton) not integrated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[3,4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2,9]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,2,9]}],"complexes":["SMG1C (SMG1-SMG8-SMG9)"],"partners":["SMG1","SMG8","UPF1","IQGAP1","GPX4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H0W8","full_name":"Nonsense-mediated mRNA decay factor SMG9","aliases":[],"length_aa":520,"mass_kda":57.7,"function":"Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons (PubMed:19417104). Is recruited by release factors to stalled ribosomes together with SMG1 and SMG8 (forming the SMG1C protein kinase complex) and, in the SMG1C complex, is required for the efficient association between SMG1 and SMG8 (PubMed:19417104). Plays a role in brain, heart, and eye development (By similarity)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9H0W8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SMG9","classification":"Not Classified","n_dependent_lines":22,"n_total_lines":1208,"dependency_fraction":0.018211920529801324},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SMG9","total_profiled":1310},"omim":[{"mim_id":"619995","title":"NEURODEVELOPMENTAL DISORDER WITH INTENTION TREMOR, PYRAMIDAL SIGNS, DYSPRAXIA, AND OCULAR ANOMALIES; NEDITPO","url":"https://www.omim.org/entry/619995"},{"mim_id":"616920","title":"HEART AND BRAIN MALFORMATION SYNDROME; HBMS","url":"https://www.omim.org/entry/616920"},{"mim_id":"613176","title":"SMG9 NONSENSE-MEDIATED mRNA DECAY FACTOR; SMG9","url":"https://www.omim.org/entry/613176"},{"mim_id":"613175","title":"SMG8 NONSENSE-MEDIATED mRNA DECAY FACTOR; SMG8","url":"https://www.omim.org/entry/613175"},{"mim_id":"607032","title":"SMG1 NONSENSE-MEDIATED mRNA DECAY-ASSOCIATED PI3K-RELATED KINASE; SMG1","url":"https://www.omim.org/entry/607032"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SMG9"},"hgnc":{"alias_symbol":["FLJ12886"],"prev_symbol":["C19orf61"]},"alphafold":{"accession":"Q9H0W8","domains":[{"cath_id":"3.40.50.300","chopping":"180-344_362-434_459-518","consensus_level":"high","plddt":90.2683,"start":180,"end":518}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H0W8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H0W8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H0W8-F1-predicted_aligned_error_v6.png","plddt_mean":70.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SMG9","jax_strain_url":"https://www.jax.org/strain/search?query=SMG9"},"sequence":{"accession":"Q9H0W8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H0W8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H0W8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H0W8"}},"corpus_meta":[{"pmid":"19417104","id":"PMC_19417104","title":"SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay.","date":"2009","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/19417104","citation_count":199,"is_preprint":false},{"pmid":"20817927","id":"PMC_20817927","title":"Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex.","date":"2010","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/20817927","citation_count":73,"is_preprint":false},{"pmid":"26130714","id":"PMC_26130714","title":"A network of SMG-8, SMG-9 and SMG-1 C-terminal insertion domain regulates UPF1 substrate recruitment and phosphorylation.","date":"2015","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/26130714","citation_count":52,"is_preprint":false},{"pmid":"34146907","id":"PMC_34146907","title":"SMG9 drives ferroptosis by directly inhibiting GPX4 degradation.","date":"2021","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/34146907","citation_count":38,"is_preprint":false},{"pmid":"31792449","id":"PMC_31792449","title":"InsP6 binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex.","date":"2019","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/31792449","citation_count":31,"is_preprint":false},{"pmid":"31729466","id":"PMC_31729466","title":"Cryo-EM structure of SMG1-SMG8-SMG9 complex.","date":"2019","source":"Cell research","url":"https://pubmed.ncbi.nlm.nih.gov/31729466","citation_count":27,"is_preprint":false},{"pmid":"36273494","id":"PMC_36273494","title":"SMG8/SMG9 Heterodimer Loss Modulates SMG1 Kinase to Drive ATR Inhibitor Resistance.","date":"2022","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/36273494","citation_count":14,"is_preprint":false},{"pmid":"35087184","id":"PMC_35087184","title":"A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development.","date":"2022","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/35087184","citation_count":12,"is_preprint":false},{"pmid":"28389433","id":"PMC_28389433","title":"Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins.","date":"2017","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/28389433","citation_count":11,"is_preprint":false},{"pmid":"21640080","id":"PMC_21640080","title":"Role of a tyrosine phosphorylation of SMG-9 in binding of SMG-9 to IQGAP and the NMD complex.","date":"2011","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/21640080","citation_count":7,"is_preprint":false},{"pmid":"30902786","id":"PMC_30902786","title":"MicroRNA 4651 regulates nonsense-mediated mRNA decay by targeting SMG9 mRNA.","date":"2019","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/30902786","citation_count":5,"is_preprint":false},{"pmid":"34761517","id":"PMC_34761517","title":"Expanding the phenotypic and allelic spectrum of SMG8: Clinical observations reveal overlap with SMG9-associated disease trait.","date":"2021","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/34761517","citation_count":5,"is_preprint":false},{"pmid":"34456727","id":"PMC_34456727","title":"SMG9 Serves as an Oncogene to Promote the Tumor Progression via EMT and Wnt/β-Catenin Signaling Pathway in Hepatocellular Carcinoma.","date":"2021","source":"Frontiers in pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/34456727","citation_count":4,"is_preprint":false},{"pmid":"35321723","id":"PMC_35321723","title":"Identification of a novel compound heterozygous SMG9 variants in a Chinese family with heart and brain malformation syndrome using whole exome sequencing.","date":"2022","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/35321723","citation_count":2,"is_preprint":false},{"pmid":"41830328","id":"PMC_41830328","title":"SMG1:SMG8:SMG9-complex integrity supports efficient execution of nonsense-mediated mRNA decay.","date":"2026","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/41830328","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9221,"output_tokens":2887,"usd":0.035484,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10216,"output_tokens":3234,"usd":0.065965,"stage2_stop_reason":"end_turn"},"total_usd":0.101449,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2009,\n      \"finding\": \"SMG-9 (together with SMG-8) was identified as a novel subunit of the SMG-1 kinase complex; SMG-8 and SMG-9 suppress SMG-1 kinase activity in the isolated SMG-1 complex and are involved in NMD in both mammals and nematodes. SMG-8 recruits SMG-1 to the mRNA surveillance complex.\",\n      \"method\": \"Co-immunoprecipitation, functional RNAi knockdown in mammals and C. elegans, biochemical fractionation\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, multiple orthogonal methods (kinase assays, RNAi in two organisms), replicated across labs subsequently\",\n      \"pmids\": [\"19417104\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"SMG-9 comprises an N-terminal intrinsically disordered region (IDR, ~180 residues) followed by a well-folded C-terminal domain; both domains are required for SMG-1 binding and SMG1C complex integrity, whereas the C-terminus alone is sufficient to interact with SMG-8. SMG-9 also forms SMG-9:SMG-9 homo-oligomers and SMG-8:SMG-9 complexes that are distinct from SMG1C.\",\n      \"method\": \"Biochemical domain-deletion mapping, co-immunoprecipitation, biophysical characterization (SEC, limited proteolysis), electron microscopy\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal biochemical methods (deletion mapping, Co-IP, EM), single lab but comprehensive domain dissection\",\n      \"pmids\": [\"20817927\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Cryo-EM of the SMG-1-8-9-UPF1 complex revealed that UPF1 is recruited to both the SMG-1 kinase domain and C-terminal insertion domain, inducing opening of the head domain to expose the active site. SMG-8 and SMG-9 interact with the SMG-1 C-insertion domain, promoting high-affinity UPF1 binding while decelerating SMG-1 kinase activity and enhancing stringency of phosphorylation site selection. UPF2 binding destabilizes the SMG-1-8-9-UPF1 complex, promoting substrate release.\",\n      \"method\": \"Electron cryo-microscopy (cryo-EM) of SMG-1-8-9-UPF1 complex, biochemical binding assays, kinase activity assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structural analysis combined with biochemical kinase assays, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"26130714\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structure (2.5 Å) of the SMG8-SMG9 core complex from C. elegans revealed a G-domain heterodimer with architectural similarity to dynamin-like GTPases (Atlastin, GBP1). Nucleotide binding occurs at the G domain of SMG9 but not of SMG8. The heterodimer forms in the absence of nucleotides, with interactions conserved from worms to humans.\",\n      \"method\": \"X-ray crystallography (2.5 Å), nucleotide-binding assays, fitting into EM densities of human SMG1-SMG8-SMG9\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — atomic-resolution crystal structure with functional nucleotide-binding validation, single lab\",\n      \"pmids\": [\"28389433\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Cryo-EM structure (3.4 Å) of the human SMG1-SMG8-SMG9 complex showed that SMG8 contains a C-terminal kinase inhibitory domain (KID) that covers the catalytic pocket of SMG1. Structural analysis suggested GTP hydrolysis by SMG9 would cause a conformational change moving the KID away from the inhibitory position to restore SMG1 kinase activity.\",\n      \"method\": \"Cryo-EM (3.4 Å and 3.6 Å resolution), biochemical kinase inhibition assays\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — near-atomic cryo-EM structures independently determined by two groups (PMIDs 31729466 and 31792449) in the same year\",\n      \"pmids\": [\"31729466\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Cryo-EM structure (3.45 Å) of human SMG1-SMG8-SMG9 combined with MS analysis revealed the presence of inositol hexaphosphate (InsP6) bound in the SMG1 kinase; the InsP6-binding site is required for optimal in vitro phosphorylation of SMG1 substrates.\",\n      \"method\": \"Cryo-EM (3.45 Å), mass spectrometry, in vitro kinase activity assays with InsP6-binding site mutants\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution structure plus MS plus functional mutagenesis, replicated structural finding across two contemporaneous studies\",\n      \"pmids\": [\"31792449\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SMG-9 is tyrosine-phosphorylated at Tyr-41; phosphorylation at this site regulates binding of SMG-9 to IQGAP1, an actin cytoskeleton modifier. SMG-9 co-localizes with IQGAP1 at sites of actin enrichment in non-stimulated cells but not in EGF-stimulated cells. EGF stimulation increases the ability of SMG-9 to bind SMG-8.\",\n      \"method\": \"Co-immunoprecipitation, phospho-site mutagenesis (Tyr-41), immunofluorescence co-localization, EGF stimulation assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-IP with mutagenesis and co-localization, single lab, limited orthogonal validation\",\n      \"pmids\": [\"21640080\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SMG9 directly binds GPX4 and promotes its degradation in response to the GPX4 inhibitor RSL3 (but not erastin). Genetic inhibition of SMG9 increases GPX4 accumulation specifically in mitochondria, preventing mitochondrial oxidative damage and conferring ferroptosis resistance. This function is independent of SMG9's role in NMD.\",\n      \"method\": \"RNAi screen, co-immunoprecipitation (SMG9-GPX4 direct binding), siRNA knockdown, subcellular fractionation (mitochondrial GPX4 accumulation), xenograft mouse models\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP demonstrating direct binding plus functional loss-of-function phenotype in vitro and in vivo, single lab, limited mechanistic detail on degradation mechanism\",\n      \"pmids\": [\"34146907\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Loss-of-function mutations in SMG9 (or SMG8) cause ATR inhibitor resistance through an SMG1-mediated mechanism. SMG8/9-deficient cells showed reduced ATRi-induced transcription/replication conflicts (TRCs) and lacked characteristic ATRi-induced DNA damage signaling changes (ATM/CHK2, γH2AX, phospho-RPA, 53BP1), establishing SMG8/SMG9/SMG1 pathway involvement in the cellular response to replication stress.\",\n      \"method\": \"Genome-wide CRISPR-Cas9 resistance screen, loss-of-function genetic validation, cell cycle analysis, DNA damage marker immunofluorescence, TRC measurement assays\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide CRISPR screen followed by genetic validation and multiple phenotypic readouts, single lab\",\n      \"pmids\": [\"36273494\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Complete deletion of SMG9 (or SMG8) in human cells caused only modest NMD impairment with moderately increased UPF1 phosphorylation. Deletion of the SMG8 kinase inhibitory domain (KID) alone did not affect UPF1 phosphorylation or NMD efficiency, demonstrating the KID is dispensable in vivo. However, SMG9-deficient (and SMG8-deficient) cells showed pronounced hypersensitivity to partial pharmacological SMG1 inhibition, establishing SMG8 and SMG9 as nonessential modulators that safeguard NMD efficiency and perturbation tolerance.\",\n      \"method\": \"CRISPR-Cas9 gene deletion, pharmacological SMG1 inhibition, RNA-seq transcriptome-wide NMD target analysis, UPF1 phosphorylation western blot, multiple human cell lines\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic KO combined with pharmacological perturbation and transcriptome-wide readout across multiple cell lines, comprehensive dissection\",\n      \"pmids\": [\"41830328\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SMG9 is a regulatory subunit of the SMG1C kinase complex (SMG1-SMG8-SMG9) that forms a G-domain heterodimer with SMG8; SMG9's GTPase domain promotes conformational changes that relieve SMG8-mediated inhibition of SMG1's catalytic pocket, while together SMG8 and SMG9 modulate UPF1 substrate recruitment and phosphorylation stringency to safeguard nonsense-mediated mRNA decay efficiency. Beyond NMD, SMG9 is tyrosine-phosphorylated at Tyr-41 to regulate IQGAP1 binding and actin cytoskeleton association, directly binds and promotes mitochondrial GPX4 degradation to drive ferroptosis, and its loss confers ATR inhibitor resistance via an SMG1-dependent mechanism.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SMG9 is a regulatory subunit of the SMG1 kinase complex (SMG1C) that safeguards the efficiency of nonsense-mediated mRNA decay (NMD) [#0, #9]. Together with SMG8, SMG9 was identified as a component of the SMG1 complex that suppresses SMG1 kinase activity and is required for NMD in mammals and nematodes [#0]. SMG9 consists of an N-terminal intrinsically disordered region and a folded C-terminal domain, both required for SMG1 binding and SMG1C integrity, while its C-terminus mediates interaction with SMG8 [#1]. The SMG8-SMG9 pair forms a G-domain heterodimer architecturally related to dynamin-like GTPases, with nucleotide binding occurring at the SMG9 G domain but not SMG8 [#3]. Within SMG1C, SMG8 carries a C-terminal kinase inhibitory domain (KID) that occludes the SMG1 catalytic pocket, and structural analysis indicates GTP hydrolysis by SMG9 repositions the KID to restore kinase activity [#4]. During substrate engagement, SMG8 and SMG9 promote high-affinity UPF1 binding while decelerating SMG1 and enhancing the stringency of phosphorylation-site selection [#2]. Genetic deletion of SMG9 causes only modest NMD impairment with moderately elevated UPF1 phosphorylation, establishing SMG8 and SMG9 as nonessential modulators that buffer NMD against perturbation, since SMG9-deficient cells are hypersensitive to partial SMG1 inhibition [#9]. Beyond NMD, SMG9 is tyrosine-phosphorylated at Tyr-41 to regulate IQGAP1 binding and actin-cytoskeleton association [#6], directly binds GPX4 to promote its mitochondrial degradation and drive ferroptosis [#7], and its loss confers ATR-inhibitor resistance through an SMG1-dependent effect on replication stress signaling [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established SMG9 as a bona fide subunit of the SMG1 kinase complex and a functional NMD factor, defining its core biological context.\",\n      \"evidence\": \"Co-IP, RNAi knockdown in mammals and C. elegans, biochemical fractionation\",\n      \"pmids\": [\"19417104\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of kinase suppression not resolved\", \"Domain requirements for complex assembly undefined\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Resolved SMG9's domain organization, showing both its IDR and folded C-terminus are required for SMG1C integrity while the C-terminus alone binds SMG8.\",\n      \"evidence\": \"Domain-deletion mapping, Co-IP, SEC, limited proteolysis, EM\",\n      \"pmids\": [\"20817927\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional role of SMG9 homo-oligomers and SMG8:SMG9 sub-complexes unknown\", \"No atomic structure of the interfaces\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined how SMG8/SMG9 shape catalysis by showing they promote high-affinity UPF1 recruitment while decelerating SMG1 and sharpening phosphosite selection, with UPF2 triggering substrate release.\",\n      \"evidence\": \"Cryo-EM of SMG1-8-9-UPF1, binding and kinase assays\",\n      \"pmids\": [\"26130714\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"SMG9-specific contributions not separated from SMG8\", \"Conformational dynamics not captured at high resolution\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Revealed the SMG8-SMG9 core as a G-domain heterodimer resembling dynamin-like GTPases, localizing nucleotide binding to SMG9, providing a structural basis for a GTPase-driven regulatory switch.\",\n      \"evidence\": \"X-ray crystallography (2.5 Å) of C. elegans SMG8-SMG9, nucleotide-binding assays, EM fitting\",\n      \"pmids\": [\"28389433\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"GTP hydrolysis activity and turnover not measured\", \"Coupling of nucleotide state to kinase regulation untested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Connected SMG9's GTPase domain to kinase control by showing SMG8's KID occludes the SMG1 catalytic pocket and that SMG9-driven conformational change would relieve this inhibition; an InsP6 cofactor supports optimal substrate phosphorylation.\",\n      \"evidence\": \"Cryo-EM (3.4–3.45 Å) of human SMG1-8-9, MS, kinase assays with InsP6-site mutants\",\n      \"pmids\": [\"31729466\", \"31792449\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct demonstration that SMG9 GTP hydrolysis triggers KID release in vivo absent\", \"Timing of the switch during NMD undefined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identified a non-NMD activity in which Tyr-41 phosphorylation of SMG9 governs binding to the actin modifier IQGAP1, implicating SMG9 in cytoskeletal signaling.\",\n      \"evidence\": \"Co-IP, Tyr-41 phospho-mutagenesis, immunofluorescence, EGF stimulation\",\n      \"pmids\": [\"21640080\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinase responsible for Tyr-41 phosphorylation unknown\", \"Functional consequence for actin dynamics not established\", \"Single lab, limited orthogonal validation\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed an NMD-independent role: SMG9 directly binds GPX4 and promotes its mitochondrial degradation, sensitizing cells to RSL3-induced ferroptosis.\",\n      \"evidence\": \"RNAi screen, Co-IP, siRNA knockdown, subcellular fractionation, xenografts\",\n      \"pmids\": [\"34146907\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of GPX4 degradation not defined\", \"How SMG9 distinguishes mitochondrial GPX4 pools unclear\", \"Single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked SMG9 to replication stress responses by showing its loss causes ATR-inhibitor resistance via an SMG1-mediated reduction in transcription-replication conflicts and DNA damage signaling.\",\n      \"evidence\": \"Genome-wide CRISPR resistance screen, genetic validation, DNA damage marker IF, TRC assays\",\n      \"pmids\": [\"36273494\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular target of SMG1 in this pathway unidentified\", \"Whether the role requires NMD vs. a direct activity unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Reframed SMG9 (and SMG8) as nonessential NMD modulators by showing their deletion only modestly impairs NMD but sensitizes cells to partial SMG1 inhibition, and that the SMG8 KID is dispensable in vivo.\",\n      \"evidence\": \"CRISPR KO, pharmacological SMG1 inhibition, RNA-seq, UPF1 phospho-blot across cell lines\",\n      \"pmids\": [\"41830328\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo trigger and timing of the GTPase switch still undefined\", \"Reconciliation of dispensable KID with structural inhibition model incomplete\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether and how SMG9 GTP hydrolysis is catalytically coupled to relief of SMG8-mediated kinase inhibition during a physiological NMD cycle remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No measurement of SMG9 GTPase turnover within active SMG1C in cells\", \"Mechanistic basis of NMD-independent functions (ferroptosis, replication stress, cytoskeleton) not integrated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 2, 9]}\n    ],\n    \"complexes\": [\"SMG1C (SMG1-SMG8-SMG9)\"],\n    \"partners\": [\"SMG1\", \"SMG8\", \"UPF1\", \"IQGAP1\", \"GPX4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}