{"gene":"PSMG4","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2007,"finding":"PAC4 (PSMG4) was identified as a mammalian proteasome assembly chaperone functioning as part of the PAC3-PAC4 heterodimer pair, acting at early stages of 20S proteasome assembly (alpha-ring formation), analogous to yeast Poc3/Poc4. It works upstream of the half-proteasome maturase UMP1.","method":"Genetic phenotype screen, yeast and mammalian cell-based functional complementation, identification of functional homologs","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal approaches across yeast and mammalian systems, replicated across labs in subsequent studies","pmids":["17707236"],"is_preprint":false},{"year":2008,"finding":"PAC3-PAC4 heterodimer promotes assembly of rings composed of seven alpha subunits of the 20S proteasome core particle, acting prior to beta-subunit incorporation and prior to UMP1-dependent half-proteasome dimerization.","method":"Biochemical fractionation, assembly intermediate analysis, review/synthesis of experimental data","journal":"Structure (London, England : 1993)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — synthesis of multiple experimental studies, but this paper is a review/perspective rather than primary experimental data","pmids":["18786393"],"is_preprint":false},{"year":2010,"finding":"PAC3-PAC4 heterodimer is implicated in alpha-ring formation during 20S proteasome core particle assembly; PAC3-PAC4 acts upstream of beta-subunit incorporation and UMP1 function.","method":"Biochemical analysis of assembly intermediates, review of experimental data","journal":"Biochemical Society transactions","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — review synthesizing multiple experimental results; corroborates primary data from other papers","pmids":["20074030"],"is_preprint":false},{"year":2017,"finding":"Crystal structure of human PAC4 (PSMG4) determined at 1.90-Å resolution, revealing a hydrophobic surface surrounded by charged residues that is complementary to its binding partner PAC3 and exhibits charge complementarity with proteasomal α4-5 subunits.","method":"X-ray crystallography at 1.90-Å resolution","journal":"Protein science : a publication of the Protein Society","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution crystal structure with surface characterization identifying binding interfaces","pmids":["28263418"],"is_preprint":false},{"year":2018,"finding":"PAC3-PAC4 is required for formation of the core α4-α7 intermediate as the initial step of α-ring assembly. Without PAC3-PAC4, the α4-α7 core intermediate does not form. PAC1-PAC2 then prevents nonproductive dimerization of α-ring assembly intermediates and retains them in the cytoplasm by overriding nuclear localization signals of α-subunits.","method":"Co-immunoprecipitation, knockdown experiments, subcellular fractionation, overexpression of assembly intermediates","journal":"Genes to cells : devoted to molecular & cellular mechanisms","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, KD, fractionation) in a single study establishing ordered assembly pathway with specific roles for PAC3-PAC4","pmids":["30133132"],"is_preprint":false},{"year":2019,"finding":"The PAC3-PAC4 heterodimer functions as a molecular matchmaker, stabilizing the α4-α5-α6 subcomplex during α-ring assembly. A 0.96-Å crystal structure of PAC3 homodimer and NMR data revealed loop mobility (residues 51-61) and enabled modeling of the PAC3-4/α4/α5/α6 quintet complex.","method":"X-ray crystallography (0.96-Å resolution), NMR spectroscopy, 3D structural modeling, biochemical binding assays","journal":"International journal of molecular sciences","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution crystal structure combined with NMR and structural modeling, directly identifying PAC4 binding interface and mechanistic role","pmids":["31067643"],"is_preprint":false},{"year":2022,"finding":"PAC3-PAC4 is required for selective incorporation of immunoproteasome-specific beta subunits (β1i, β2i) before other beta subunits during immunoproteasome assembly, providing selectivity against constitutive subunits.","method":"Biochemical assembly intermediate analysis, review of experimental data","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — review synthesizing multiple experimental findings about specialized proteasome assembly, corroborated across studies","pmids":["35563886"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structures of chaperone-bound human 20S proteasome assembly intermediates show that PAC3/PAC4 stabilizes an early α-ring intermediate subcomplex together with PAC1-PAC2. Dissociation of PAC3/PAC4 (along with rearrangement of PAC1 N-terminal tail) triggers the transition to β-ring assembly. Completion of β-ring and half-proteasome dimerization repositions lysine K33 to trigger β pro-peptide cleavage, leading to concerted dissociation of POMP and PAC1/PAC2.","method":"Cryo-EM of endogenously CRISPR-tagged chaperone-bound complexes, structural analysis of assembly intermediates","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structures with endogenous tagging, multiple assembly intermediates captured, mechanistic dissociation pathway defined","pmids":["39294158"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM reconstructions of seven recombinant human proteasome subcomplexes visualize PAC4 as part of the chaperone ensemble stabilizing early assembly intermediates; PAC3/PAC4 dissociation is required for progression from α-ring to β-ring assembly. Structural data explain the order of successive subunit additions and how assembly factors rearrange to coordinate proteolytic activation.","method":"Cryo-EM of recombinant human subcomplexes, structural comparison of intermediates and mature CP","journal":"bioRxiv : the preprint server for biology","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — cryo-EM structural study (preprint), consistent with published peer-reviewed findings but awaiting formal peer review","pmids":["38328185"],"is_preprint":true},{"year":2025,"finding":"CRISPR/Cas9 genome-wide knockout screen identified PSMG4 as a gene whose loss confers resistance to colibactin-induced cytotoxicity, suggesting PSMG4 participates in the cellular response pathway to colibactin-mediated DNA damage. (Note: mechanistic validation was performed for PSMD4, not PSMG4, in this study.)","method":"Genome-wide CRISPR/Cas9 knockout screen with MAGeCK scoring","journal":"mSphere","confidence":"Low","confidence_rationale":"Tier 3 / Weak — screen hit identified but not mechanistically validated for PSMG4 specifically; functional follow-up was done on PSMD4","pmids":["39918307"],"is_preprint":false},{"year":2025,"finding":"Caffeine treatment of colorectal adenocarcinoma cells decreased expression of PAC4 (PSMG4) coincident with reduced immunoproteasome content and reduced oxidative stress, suggesting PAC4 expression is linked to immunoproteasome biogenesis in cancer cells.","method":"qPCR, Western blot, transcriptome analysis, flow cytometry of proteasome subunit expression","journal":"Biochimie","confidence":"Low","confidence_rationale":"Tier 3 / Weak — correlative expression data from drug treatment; no direct manipulation of PSMG4 to establish causal mechanism","pmids":["40349826"],"is_preprint":false},{"year":2026,"finding":"Alternative splicing of Psmg4 pre-mRNA regulated by the SRSF5 splicing factor promotes exon 2 skipping, reducing full-length Psmg4 isoform expression. A tRNA-derived fragment (CHAtRF) directly interacts with SRSF5, blocking its binding to Psmg4 pre-mRNA and thereby promoting exon 2 skipping, which inhibits full-length PSMG4 expression and contributes to pathological cardiac hypertrophy.","method":"RNA pulldown/interaction assays, alternative splicing reporter assays, cardiac hypertrophy models (AngII-treated mice, hiPSC-CMs), CHAtRF overexpression/knockdown","journal":"Research (Washington, D.C.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (RNA interaction, splicing assays, in vivo and hiPSC-CM models) from a single lab establishing SRSF5-dependent alternative splicing of PSMG4","pmids":["41907183"],"is_preprint":false}],"current_model":"PSMG4 (PAC4) is a dedicated 20S proteasome assembly chaperone that forms a PAC3-PAC4 heterodimer which stabilizes early α-ring intermediates (particularly the α4-α5-α6 subcomplex) during proteasome biogenesis; cryo-EM and crystallographic structures have defined its binding interfaces with PAC3 and α-subunits, showing that PAC3/PAC4 dissociation is required for transition from α-ring to β-ring assembly, and that its full-length expression is regulated by SRSF5-dependent alternative splicing linked to cardiac hypertrophy."},"narrative":{"mechanistic_narrative":"PSMG4 (PAC4) is a dedicated proteasome assembly chaperone that operates at the earliest stage of 20S core particle biogenesis as one half of the PAC3-PAC4 heterodimer, the mammalian counterpart of yeast Poc3/Poc4 acting upstream of the half-proteasome maturase UMP1 [PMID:17707236]. The heterodimer functions as a molecular matchmaker that nucleates α-ring assembly: it is required to form the initial α4–α7 core intermediate and stabilizes the α4-α5-α6 subcomplex, without which the α-ring cannot assemble [PMID:30133132, PMID:31067643]. Atomic-resolution crystallography of human PAC4 defined a hydrophobic surface ringed by charged residues that is complementary to PAC3 and charge-complementary to the proteasomal α4-α5 subunits, providing the structural basis for these interactions [PMID:28263418, PMID:31067643]. Cryo-EM of chaperone-bound assembly intermediates places PAC3/PAC4 alongside PAC1-PAC2 on an early α-ring intermediate and shows that timed dissociation of PAC3/PAC4 is the trigger that licenses the transition from α-ring to β-ring assembly [PMID:39294158]. Beyond its constitutive role, PAC3-PAC4 also directs selective incorporation of immunoproteasome-specific β subunits during immunoproteasome assembly [PMID:35563886]. PSMG4 expression is controlled by SRSF5-dependent alternative splicing, where exon 2 skipping reduces full-length PSMG4 and contributes to pathological cardiac hypertrophy [PMID:41907183].","teleology":[{"year":2007,"claim":"Established that mammals possess a dedicated early-acting proteasome assembly chaperone, defining PAC4 as a functional homolog working with PAC3 upstream of UMP1.","evidence":"Genetic phenotype screen and functional complementation across yeast and mammalian cells","pmids":["17707236"],"confidence":"High","gaps":["Did not provide structural detail of PAC3-PAC4 interaction","Precise α-subunit binding partners not yet defined"]},{"year":2010,"claim":"Consolidated the model that PAC3-PAC4 acts in α-ring formation prior to β-subunit incorporation and UMP1 function, ordering the assembly pathway.","evidence":"Biochemical analysis of assembly intermediates synthesized in review form","pmids":["18786393","20074030"],"confidence":"Medium","gaps":["Reviews rather than new primary data","Mechanism of which α-subunits PAC3-PAC4 directly engages unresolved"]},{"year":2017,"claim":"Provided the atomic structure of human PAC4, revealing the chemical basis for its complementarity with PAC3 and proteasomal α-subunits.","evidence":"X-ray crystallography at 1.90-Å resolution with surface characterization","pmids":["28263418"],"confidence":"High","gaps":["Structure of the assembled PAC3-PAC4/α-subunit complex not determined","Dynamics of binding not addressed"]},{"year":2018,"claim":"Demonstrated that PAC3-PAC4 is strictly required to nucleate the α4–α7 core intermediate, establishing its non-redundant role at the start of α-ring assembly.","evidence":"Co-immunoprecipitation, knockdown, subcellular fractionation and overexpression of intermediates","pmids":["30133132"],"confidence":"High","gaps":["Quantitative kinetics of intermediate formation not measured","Coordination with PAC1-PAC2 retention mechanism only partly defined"]},{"year":2019,"claim":"Defined PAC3-PAC4 as a molecular matchmaker stabilizing the α4-α5-α6 subcomplex and modeled the quintet complex at atomic resolution.","evidence":"0.96-Å crystallography, NMR, structural modeling and biochemical binding assays","pmids":["31067643"],"confidence":"High","gaps":["Functional consequence of loop 51-61 mobility not directly tested","Model not confirmed by a full experimental complex structure"]},{"year":2022,"claim":"Extended PAC3-PAC4 function to specialized assembly, showing it directs selective incorporation of immunoproteasome β subunits.","evidence":"Biochemical assembly intermediate analysis synthesized in review form","pmids":["35563886"],"confidence":"Medium","gaps":["Review rather than primary data","Molecular basis for β1i/β2i selectivity not structurally defined"]},{"year":2024,"claim":"Captured the full chaperone-bound assembly trajectory, showing PAC3/PAC4 dissociation triggers the α-to-β ring transition and couples to proteolytic activation.","evidence":"Cryo-EM of endogenously CRISPR-tagged and recombinant chaperone-bound intermediates","pmids":["39294158","38328185"],"confidence":"High","gaps":["Signal that times PAC3/PAC4 release not identified","Preprint companion study awaiting peer review"]},{"year":2025,"claim":"Linked PSMG4 to cellular drug and damage responses through unbiased screens and expression correlation, though without direct mechanistic validation.","evidence":"Genome-wide CRISPR knockout screen and drug-treatment expression profiling in cancer cells","pmids":["39918307","40349826"],"confidence":"Low","gaps":["Colibactin screen validated PSMD4, not PSMG4","Caffeine data are correlative with no PSMG4 manipulation"]},{"year":2026,"claim":"Revealed regulatory control of PSMG4 abundance via SRSF5-dependent alternative splicing, connecting PSMG4 dosage to cardiac hypertrophy.","evidence":"RNA interaction assays, splicing reporters, AngII mouse and hiPSC-CM models with CHAtRF manipulation","pmids":["41907183"],"confidence":"Medium","gaps":["Whether reduced PSMG4 impairs proteasome assembly in cardiomyocytes not shown","Single-lab finding awaiting independent replication"]},{"year":null,"claim":"The molecular trigger that times PAC3/PAC4 dissociation and how PSMG4 dosage perturbations propagate to proteasome capacity in disease remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No defined signal driving PAC3/PAC4 release","Causal link between PSMG4 splicing changes and proteasome dysfunction in hypertrophy not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,4,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,4,7]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,4,7]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[4,7]}],"complexes":["PAC3-PAC4 heterodimer","20S proteasome assembly intermediate"],"partners":["PSMG3","PSMA7","PSMA5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5JS54","full_name":"Proteasome assembly chaperone 4","aliases":["Proteasome chaperone homolog 4","Pba4"],"length_aa":123,"mass_kda":13.8,"function":"Chaperone protein which promotes assembly of the 20S proteasome","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q5JS54/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PSMG4","classification":"Common Essential","n_dependent_lines":1193,"n_total_lines":1208,"dependency_fraction":0.9875827814569537},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000180822","cell_line_id":"CID000137","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":3},{"compartment":"big_aggregates","grade":2}],"interactors":[{"gene":"PSMG1","stoichiometry":10.0},{"gene":"PSMG2","stoichiometry":10.0},{"gene":"POMP","stoichiometry":10.0},{"gene":"PSMG3","stoichiometry":0.2},{"gene":"MELK","stoichiometry":0.2},{"gene":"PSMA4","stoichiometry":0.2},{"gene":"PSMA2","stoichiometry":0.2},{"gene":"PSMA5","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000137","total_profiled":1310},"omim":[{"mim_id":"617550","title":"PROTEASOME ASSEMBLY CHAPERONE 4; PSMG4","url":"https://www.omim.org/entry/617550"},{"mim_id":"617528","title":"PROTEASOME ASSEMBLY CHAPERONE 3; PSMG3","url":"https://www.omim.org/entry/617528"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Mitochondria","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PSMG4"},"hgnc":{"alias_symbol":["PAC4"],"prev_symbol":["C6orf86"]},"alphafold":{"accession":"Q5JS54","domains":[{"cath_id":"3.30.230.100","chopping":"29-121","consensus_level":"high","plddt":91.9139,"start":29,"end":121}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5JS54","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5JS54-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5JS54-F1-predicted_aligned_error_v6.png","plddt_mean":87.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PSMG4","jax_strain_url":"https://www.jax.org/strain/search?query=PSMG4"},"sequence":{"accession":"Q5JS54","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5JS54.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5JS54/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5JS54"}},"corpus_meta":[{"pmid":"17707236","id":"PMC_17707236","title":"20S proteasome assembly is orchestrated by two distinct pairs of chaperones in yeast and in mammals.","date":"2007","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/17707236","citation_count":165,"is_preprint":false},{"pmid":"21249144","id":"PMC_21249144","title":"Identification of genes that elicit disuse muscle atrophy via the transcription factors p50 and Bcl-3.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21249144","citation_count":68,"is_preprint":false},{"pmid":"18786393","id":"PMC_18786393","title":"PACemakers of proteasome core particle assembly.","date":"2008","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/18786393","citation_count":51,"is_preprint":false},{"pmid":"3428258","id":"PMC_3428258","title":"A complex gene superfamily encodes actin in petunia.","date":"1987","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/3428258","citation_count":47,"is_preprint":false},{"pmid":"6683604","id":"PMC_6683604","title":"Platelet associated immunoglobulins and complement in idiopathic thrombocytopenic purpura.","date":"1983","source":"Clinical and experimental immunology","url":"https://pubmed.ncbi.nlm.nih.gov/6683604","citation_count":30,"is_preprint":false},{"pmid":"30133132","id":"PMC_30133132","title":"PAC1-PAC2 proteasome assembly chaperone retains the core α4-α7 assembly intermediates in the cytoplasm.","date":"2018","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/30133132","citation_count":27,"is_preprint":false},{"pmid":"35563886","id":"PMC_35563886","title":"The Molecular Mechanisms Governing the Assembly of the Immuno- and Thymoproteasomes in the Presence of Constitutive Proteasomes.","date":"2022","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/35563886","citation_count":25,"is_preprint":false},{"pmid":"31067643","id":"PMC_31067643","title":"Molecular and Structural Basis of the Proteasome α Subunit Assembly Mechanism Mediated by the Proteasome-Assembling Chaperone PAC3-PAC4 Heterodimer.","date":"2019","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/31067643","citation_count":23,"is_preprint":false},{"pmid":"35585482","id":"PMC_35585482","title":"Sperm DNA methylation patterns at discrete CpGs and genes involved in embryonic development are related to bull fertility.","date":"2022","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/35585482","citation_count":23,"is_preprint":false},{"pmid":"20074030","id":"PMC_20074030","title":"Chaperone-assisted assembly of the proteasome core particle.","date":"2010","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/20074030","citation_count":23,"is_preprint":false},{"pmid":"1977797","id":"PMC_1977797","title":"Six actin gene subfamilies map to five chromosomes of Petunia hybrida.","date":"1990","source":"The Journal of heredity","url":"https://pubmed.ncbi.nlm.nih.gov/1977797","citation_count":16,"is_preprint":false},{"pmid":"39294158","id":"PMC_39294158","title":"Structural basis of human 20S proteasome biogenesis.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39294158","citation_count":13,"is_preprint":false},{"pmid":"28263418","id":"PMC_28263418","title":"Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation.","date":"2017","source":"Protein science : a publication of the Protein Society","url":"https://pubmed.ncbi.nlm.nih.gov/28263418","citation_count":11,"is_preprint":false},{"pmid":"32568332","id":"PMC_32568332","title":"Design of potent ABA receptor antagonists based on a conformational restriction approach.","date":"2020","source":"Organic & biomolecular chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32568332","citation_count":7,"is_preprint":false},{"pmid":"39918307","id":"PMC_39918307","title":"Genome-scale CRISPR/Cas9 screening reveals the role of PSMD4 in colibactin-mediated cell cycle arrest.","date":"2025","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/39918307","citation_count":6,"is_preprint":false},{"pmid":"40301754","id":"PMC_40301754","title":"A genome-wide association study identified candidate genes associated with egg quality traits in Muscovy duck.","date":"2025","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/40301754","citation_count":6,"is_preprint":false},{"pmid":"37176306","id":"PMC_37176306","title":"Antimicrobial Activity and Cytotoxicity of Prepolymer Allyl 2-cyanoacrylate and 2-Octyl Cyanoacrylate Mixture Adhesives for Topical Wound Closure.","date":"2023","source":"Materials (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/37176306","citation_count":3,"is_preprint":false},{"pmid":"39211201","id":"PMC_39211201","title":"Structural basis of human 20S proteasome biogenesis.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39211201","citation_count":1,"is_preprint":false},{"pmid":"40349826","id":"PMC_40349826","title":"Caffeine modulates immunoproteasome activity and content in colorectal adenocarcinoma cells.","date":"2025","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/40349826","citation_count":1,"is_preprint":false},{"pmid":"38328185","id":"PMC_38328185","title":"Visualizing chaperone-mediated multistep assembly of the human 20S proteasome.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38328185","citation_count":1,"is_preprint":false},{"pmid":"41907183","id":"PMC_41907183","title":"CHAtRF Modulates Cardiac Hypertrophy via SRSF5-Dependent Regulation of Psmg4 Alternative Splicing.","date":"2026","source":"Research (Washington, D.C.)","url":"https://pubmed.ncbi.nlm.nih.gov/41907183","citation_count":0,"is_preprint":false},{"pmid":"40338343","id":"PMC_40338343","title":"Molecular and functional analysis of a putative pyocin S9, with endonuclease activity from P. chlororaphis subsp aurantiaca PB-St2.","date":"2025","source":"Archives of microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/40338343","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12643,"output_tokens":2861,"usd":0.040422,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10341,"output_tokens":2860,"usd":0.061602,"stage2_stop_reason":"end_turn"},"total_usd":0.102024,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"PAC4 (PSMG4) was identified as a mammalian proteasome assembly chaperone functioning as part of the PAC3-PAC4 heterodimer pair, acting at early stages of 20S proteasome assembly (alpha-ring formation), analogous to yeast Poc3/Poc4. It works upstream of the half-proteasome maturase UMP1.\",\n      \"method\": \"Genetic phenotype screen, yeast and mammalian cell-based functional complementation, identification of functional homologs\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal approaches across yeast and mammalian systems, replicated across labs in subsequent studies\",\n      \"pmids\": [\"17707236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PAC3-PAC4 heterodimer promotes assembly of rings composed of seven alpha subunits of the 20S proteasome core particle, acting prior to beta-subunit incorporation and prior to UMP1-dependent half-proteasome dimerization.\",\n      \"method\": \"Biochemical fractionation, assembly intermediate analysis, review/synthesis of experimental data\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — synthesis of multiple experimental studies, but this paper is a review/perspective rather than primary experimental data\",\n      \"pmids\": [\"18786393\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PAC3-PAC4 heterodimer is implicated in alpha-ring formation during 20S proteasome core particle assembly; PAC3-PAC4 acts upstream of beta-subunit incorporation and UMP1 function.\",\n      \"method\": \"Biochemical analysis of assembly intermediates, review of experimental data\",\n      \"journal\": \"Biochemical Society transactions\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — review synthesizing multiple experimental results; corroborates primary data from other papers\",\n      \"pmids\": [\"20074030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structure of human PAC4 (PSMG4) determined at 1.90-Å resolution, revealing a hydrophobic surface surrounded by charged residues that is complementary to its binding partner PAC3 and exhibits charge complementarity with proteasomal α4-5 subunits.\",\n      \"method\": \"X-ray crystallography at 1.90-Å resolution\",\n      \"journal\": \"Protein science : a publication of the Protein Society\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution crystal structure with surface characterization identifying binding interfaces\",\n      \"pmids\": [\"28263418\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PAC3-PAC4 is required for formation of the core α4-α7 intermediate as the initial step of α-ring assembly. Without PAC3-PAC4, the α4-α7 core intermediate does not form. PAC1-PAC2 then prevents nonproductive dimerization of α-ring assembly intermediates and retains them in the cytoplasm by overriding nuclear localization signals of α-subunits.\",\n      \"method\": \"Co-immunoprecipitation, knockdown experiments, subcellular fractionation, overexpression of assembly intermediates\",\n      \"journal\": \"Genes to cells : devoted to molecular & cellular mechanisms\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, KD, fractionation) in a single study establishing ordered assembly pathway with specific roles for PAC3-PAC4\",\n      \"pmids\": [\"30133132\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The PAC3-PAC4 heterodimer functions as a molecular matchmaker, stabilizing the α4-α5-α6 subcomplex during α-ring assembly. A 0.96-Å crystal structure of PAC3 homodimer and NMR data revealed loop mobility (residues 51-61) and enabled modeling of the PAC3-4/α4/α5/α6 quintet complex.\",\n      \"method\": \"X-ray crystallography (0.96-Å resolution), NMR spectroscopy, 3D structural modeling, biochemical binding assays\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution crystal structure combined with NMR and structural modeling, directly identifying PAC4 binding interface and mechanistic role\",\n      \"pmids\": [\"31067643\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PAC3-PAC4 is required for selective incorporation of immunoproteasome-specific beta subunits (β1i, β2i) before other beta subunits during immunoproteasome assembly, providing selectivity against constitutive subunits.\",\n      \"method\": \"Biochemical assembly intermediate analysis, review of experimental data\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — review synthesizing multiple experimental findings about specialized proteasome assembly, corroborated across studies\",\n      \"pmids\": [\"35563886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structures of chaperone-bound human 20S proteasome assembly intermediates show that PAC3/PAC4 stabilizes an early α-ring intermediate subcomplex together with PAC1-PAC2. Dissociation of PAC3/PAC4 (along with rearrangement of PAC1 N-terminal tail) triggers the transition to β-ring assembly. Completion of β-ring and half-proteasome dimerization repositions lysine K33 to trigger β pro-peptide cleavage, leading to concerted dissociation of POMP and PAC1/PAC2.\",\n      \"method\": \"Cryo-EM of endogenously CRISPR-tagged chaperone-bound complexes, structural analysis of assembly intermediates\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structures with endogenous tagging, multiple assembly intermediates captured, mechanistic dissociation pathway defined\",\n      \"pmids\": [\"39294158\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM reconstructions of seven recombinant human proteasome subcomplexes visualize PAC4 as part of the chaperone ensemble stabilizing early assembly intermediates; PAC3/PAC4 dissociation is required for progression from α-ring to β-ring assembly. Structural data explain the order of successive subunit additions and how assembly factors rearrange to coordinate proteolytic activation.\",\n      \"method\": \"Cryo-EM of recombinant human subcomplexes, structural comparison of intermediates and mature CP\",\n      \"journal\": \"bioRxiv : the preprint server for biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structural study (preprint), consistent with published peer-reviewed findings but awaiting formal peer review\",\n      \"pmids\": [\"38328185\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CRISPR/Cas9 genome-wide knockout screen identified PSMG4 as a gene whose loss confers resistance to colibactin-induced cytotoxicity, suggesting PSMG4 participates in the cellular response pathway to colibactin-mediated DNA damage. (Note: mechanistic validation was performed for PSMD4, not PSMG4, in this study.)\",\n      \"method\": \"Genome-wide CRISPR/Cas9 knockout screen with MAGeCK scoring\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — screen hit identified but not mechanistically validated for PSMG4 specifically; functional follow-up was done on PSMD4\",\n      \"pmids\": [\"39918307\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Caffeine treatment of colorectal adenocarcinoma cells decreased expression of PAC4 (PSMG4) coincident with reduced immunoproteasome content and reduced oxidative stress, suggesting PAC4 expression is linked to immunoproteasome biogenesis in cancer cells.\",\n      \"method\": \"qPCR, Western blot, transcriptome analysis, flow cytometry of proteasome subunit expression\",\n      \"journal\": \"Biochimie\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — correlative expression data from drug treatment; no direct manipulation of PSMG4 to establish causal mechanism\",\n      \"pmids\": [\"40349826\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Alternative splicing of Psmg4 pre-mRNA regulated by the SRSF5 splicing factor promotes exon 2 skipping, reducing full-length Psmg4 isoform expression. A tRNA-derived fragment (CHAtRF) directly interacts with SRSF5, blocking its binding to Psmg4 pre-mRNA and thereby promoting exon 2 skipping, which inhibits full-length PSMG4 expression and contributes to pathological cardiac hypertrophy.\",\n      \"method\": \"RNA pulldown/interaction assays, alternative splicing reporter assays, cardiac hypertrophy models (AngII-treated mice, hiPSC-CMs), CHAtRF overexpression/knockdown\",\n      \"journal\": \"Research (Washington, D.C.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (RNA interaction, splicing assays, in vivo and hiPSC-CM models) from a single lab establishing SRSF5-dependent alternative splicing of PSMG4\",\n      \"pmids\": [\"41907183\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PSMG4 (PAC4) is a dedicated 20S proteasome assembly chaperone that forms a PAC3-PAC4 heterodimer which stabilizes early α-ring intermediates (particularly the α4-α5-α6 subcomplex) during proteasome biogenesis; cryo-EM and crystallographic structures have defined its binding interfaces with PAC3 and α-subunits, showing that PAC3/PAC4 dissociation is required for transition from α-ring to β-ring assembly, and that its full-length expression is regulated by SRSF5-dependent alternative splicing linked to cardiac hypertrophy.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"PSMG4 (PAC4) is a dedicated proteasome assembly chaperone that operates at the earliest stage of 20S core particle biogenesis as one half of the PAC3-PAC4 heterodimer, the mammalian counterpart of yeast Poc3/Poc4 acting upstream of the half-proteasome maturase UMP1 [#0]. The heterodimer functions as a molecular matchmaker that nucleates α-ring assembly: it is required to form the initial α4–α7 core intermediate and stabilizes the α4-α5-α6 subcomplex, without which the α-ring cannot assemble [#4, #5]. Atomic-resolution crystallography of human PAC4 defined a hydrophobic surface ringed by charged residues that is complementary to PAC3 and charge-complementary to the proteasomal α4-α5 subunits, providing the structural basis for these interactions [#3, #5]. Cryo-EM of chaperone-bound assembly intermediates places PAC3/PAC4 alongside PAC1-PAC2 on an early α-ring intermediate and shows that timed dissociation of PAC3/PAC4 is the trigger that licenses the transition from α-ring to β-ring assembly [#7]. Beyond its constitutive role, PAC3-PAC4 also directs selective incorporation of immunoproteasome-specific β subunits during immunoproteasome assembly [#6]. PSMG4 expression is controlled by SRSF5-dependent alternative splicing, where exon 2 skipping reduces full-length PSMG4 and contributes to pathological cardiac hypertrophy [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established that mammals possess a dedicated early-acting proteasome assembly chaperone, defining PAC4 as a functional homolog working with PAC3 upstream of UMP1.\",\n      \"evidence\": \"Genetic phenotype screen and functional complementation across yeast and mammalian cells\",\n      \"pmids\": [\"17707236\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not provide structural detail of PAC3-PAC4 interaction\", \"Precise α-subunit binding partners not yet defined\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Consolidated the model that PAC3-PAC4 acts in α-ring formation prior to β-subunit incorporation and UMP1 function, ordering the assembly pathway.\",\n      \"evidence\": \"Biochemical analysis of assembly intermediates synthesized in review form\",\n      \"pmids\": [\"18786393\", \"20074030\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reviews rather than new primary data\", \"Mechanism of which α-subunits PAC3-PAC4 directly engages unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Provided the atomic structure of human PAC4, revealing the chemical basis for its complementarity with PAC3 and proteasomal α-subunits.\",\n      \"evidence\": \"X-ray crystallography at 1.90-Å resolution with surface characterization\",\n      \"pmids\": [\"28263418\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of the assembled PAC3-PAC4/α-subunit complex not determined\", \"Dynamics of binding not addressed\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrated that PAC3-PAC4 is strictly required to nucleate the α4–α7 core intermediate, establishing its non-redundant role at the start of α-ring assembly.\",\n      \"evidence\": \"Co-immunoprecipitation, knockdown, subcellular fractionation and overexpression of intermediates\",\n      \"pmids\": [\"30133132\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Quantitative kinetics of intermediate formation not measured\", \"Coordination with PAC1-PAC2 retention mechanism only partly defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined PAC3-PAC4 as a molecular matchmaker stabilizing the α4-α5-α6 subcomplex and modeled the quintet complex at atomic resolution.\",\n      \"evidence\": \"0.96-Å crystallography, NMR, structural modeling and biochemical binding assays\",\n      \"pmids\": [\"31067643\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of loop 51-61 mobility not directly tested\", \"Model not confirmed by a full experimental complex structure\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended PAC3-PAC4 function to specialized assembly, showing it directs selective incorporation of immunoproteasome β subunits.\",\n      \"evidence\": \"Biochemical assembly intermediate analysis synthesized in review form\",\n      \"pmids\": [\"35563886\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Review rather than primary data\", \"Molecular basis for β1i/β2i selectivity not structurally defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Captured the full chaperone-bound assembly trajectory, showing PAC3/PAC4 dissociation triggers the α-to-β ring transition and couples to proteolytic activation.\",\n      \"evidence\": \"Cryo-EM of endogenously CRISPR-tagged and recombinant chaperone-bound intermediates\",\n      \"pmids\": [\"39294158\", \"38328185\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signal that times PAC3/PAC4 release not identified\", \"Preprint companion study awaiting peer review\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linked PSMG4 to cellular drug and damage responses through unbiased screens and expression correlation, though without direct mechanistic validation.\",\n      \"evidence\": \"Genome-wide CRISPR knockout screen and drug-treatment expression profiling in cancer cells\",\n      \"pmids\": [\"39918307\", \"40349826\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Colibactin screen validated PSMD4, not PSMG4\", \"Caffeine data are correlative with no PSMG4 manipulation\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Revealed regulatory control of PSMG4 abundance via SRSF5-dependent alternative splicing, connecting PSMG4 dosage to cardiac hypertrophy.\",\n      \"evidence\": \"RNA interaction assays, splicing reporters, AngII mouse and hiPSC-CM models with CHAtRF manipulation\",\n      \"pmids\": [\"41907183\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether reduced PSMG4 impairs proteasome assembly in cardiomyocytes not shown\", \"Single-lab finding awaiting independent replication\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular trigger that times PAC3/PAC4 dissociation and how PSMG4 dosage perturbations propagate to proteasome capacity in disease remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No defined signal driving PAC3/PAC4 release\", \"Causal link between PSMG4 splicing changes and proteasome dysfunction in hypertrophy not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 4, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 4, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 4, 7]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [4, 7]}\n    ],\n    \"complexes\": [\"PAC3-PAC4 heterodimer\", \"20S proteasome assembly intermediate\"],\n    \"partners\": [\"PSMG3\", \"PSMA7\", \"PSMA5\"],\n    \"other_free_text\": []\n  }\n}\n```","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}