{"gene":"PAIP1","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2002,"finding":"Paip1 contains two independent PABP-binding motifs: PAM2 (a 15-amino-acid stretch in the N-terminus) and PAM1 (a larger C-terminal acidic-amino-acid-rich region). PABP reciprocally contains two Paip1-binding sites: one in RNA recognition motifs 1 and 2, and one in its C-terminal domain. Paip1 binds PABP with 1:1 stoichiometry and an apparent Kd of 1.9 nM.","method":"Far-Western, GST pull-down, and surface plasmon resonance assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal in vitro binding assays (far-Western, GST pulldown, SPR) with quantitative affinity measurement; single lab but three independent methods","pmids":["11997512"],"is_preprint":false},{"year":2014,"finding":"Paip1 interacts with the eIF3g subunit of eIF3, and this interaction is regulated by amino acids through the mTORC1/S6K1/2 signaling pathway. S6K1/2 phosphorylate eIF3 to promote Paip1-eIF3 interaction, enhancing translation initiation. Rapamycin, PP242, and S6K inhibitors impair the Paip1-eIF3 interaction, and S6K inhibition reduces Paip1-stimulated translation.","method":"Co-immunoprecipitation, shRNA knockdown of S6K1/2, in vitro phosphorylation assay, translation assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP, in vitro kinase assay, genetic (shRNA) perturbation, and functional translation readout; single lab but multiple orthogonal methods","pmids":["24396066"],"is_preprint":false},{"year":2014,"finding":"The HECT-type E3 ubiquitin ligase WWP2 interacts with Paip1 via its WW domain binding to the PAM2 motif (specifically the two consecutive PXXY motifs) of Paip1, targeting Paip1 for ubiquitination and proteasomal degradation, thereby reducing Paip1-stimulated translation.","method":"Co-immunoprecipitation, ubiquitination assay, domain mapping, proteasome inhibitor treatment, translation assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping, functional ubiquitination assay, and translation readout; single lab but multiple orthogonal methods","pmids":["25266661"],"is_preprint":false},{"year":2019,"finding":"PAIP1 and PAIP2 inhibit PABP-dependent translation termination by competing with eRF3 for binding to the C-terminal domain of PABP. PAIP1 also directly binds eRF3 in solution, which stabilizes the post-termination complex. When PABP is bound to the poly(A) tail, it becomes insensitive to PAIPs and efficiently activates translation termination.","method":"In vitro translation termination assay, biochemical binding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstituted translation termination assay with direct binding measurements; single lab, multiple assay conditions","pmids":["30992367"],"is_preprint":false},{"year":2019,"finding":"PAIP1 interacts with YBX2 in vitro and in vivo in murine testes, and PAIP1 co-localizes with YBX2 in round spermatids. PAIP1 relieves YBX2-mediated translational repression of spermiogenic mRNAs bearing the YBX2 target sequence, as demonstrated by sequential RNA immunoprecipitation and in vitro translation assays.","method":"Co-immunoprecipitation, colocalization (immunofluorescence), sequential RNA immunoprecipitation, in vitro translation assay","journal":"Biology of reproduction","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and functional in vitro translation rescue; single lab, multiple orthogonal methods","pmids":["30295753"],"is_preprint":false},{"year":2021,"finding":"The SARS-CoV SUD (macrodomain II, Mac2) directly interacts with the middle domain of Paip1, and the crystal structure of this complex was determined by X-ray crystallography and validated by small-angle X-ray scattering. This interaction is conserved with SARS-CoV-2. SUD enhances viral (but not host) protein synthesis via Paip1 binding in replicon-transfected cells.","method":"Size-exclusion chromatography, split-YFP, co-immunoprecipitation, X-ray crystallography, small-angle X-ray scattering, replicon translation assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with SAXS validation, multiple binding assays (SEC, split-YFP, Co-IP), and functional in cellulo translation readout; single lab but multiple highly rigorous orthogonal methods","pmids":["33876849"],"is_preprint":false},{"year":2023,"finding":"In Drosophila, loss of Paip1 causes reduced protein translation, activates the integrated stress response (ISR) via PERK-mediated eIF2α phosphorylation, and leads to apoptotic cell death. Loss of Paip1 also upregulates the transcription factor Xrp1, whose translation is enhanced via its 5'UTR, and Xrp1 in turn contributes to eIF2α phosphorylation and apoptosis.","method":"Genetic loss-of-function (Drosophila knockdown/knockout), epistasis analysis, eIF2α phosphorylation assay, 5'UTR reporter assay","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis in Drosophila model organism with multiple downstream pathway readouts; single lab","pmids":["37543696"],"is_preprint":false},{"year":2009,"finding":"The middle domain of Paip1 (Paip1M) was crystallized and produced diffraction data to 2.2 Å resolution, providing structural information on this domain.","method":"X-ray crystallography (preliminary diffraction analysis)","journal":"Acta crystallographica. Section F","confidence":"Low","confidence_rationale":"Tier 1 / Weak — preliminary crystallographic data only, no functional validation reported in this communication","pmids":["19851022"],"is_preprint":false},{"year":2024,"finding":"PAIP1 binds directly to pre-mRNAs/mRNAs with enrichment at coding regions and introns (GA-rich splicing enhancer motifs), interacts with spliceosome components and splicing factors (by proteomics), and regulates alternative splicing of cancer-related genes including VEGFA. Deletion of a PAIP1-binding GA-repeat motif reduced PAIP1-mediated suppression of VEGFA exon 6 inclusion.","method":"iRIP-seq (UV cross-linking RNA immunoprecipitation sequencing), RNA-seq, proteomic analysis of PAIP1-interacting proteins, splicing reporter with binding-site deletion","journal":"BMC genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — iRIP-seq with RNA-seq and functional splicing reporter mutagenesis; single lab, multiple orthogonal methods","pmids":["39363305"],"is_preprint":false},{"year":2024,"finding":"PAIP1 knockdown in breast cancer cells reduces cyclin E2 (CCNE2) expression by decreasing the mRNA stability of CCNE2, leading to cell cycle arrest and inhibition of proliferation.","method":"RNA-seq, mRNA stability assay (knockdown), western blot, xenograft model","journal":"Molecular carcinogenesis","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mRNA stability assay without direct mechanistic demonstration of PAIP1-CCNE2 mRNA interaction","pmids":["39259041"],"is_preprint":false}],"current_model":"PAIP1 is a translation stimulator that binds PABP via two independent motifs (PAM1 and PAM2) and also interacts with eIF3 (via eIF3g) in an mTORC1/S6K-regulated manner to enhance cap-dependent translation initiation through mRNA circularization; its activity is negatively regulated by WWP2-mediated ubiquitination and proteasomal degradation; it also modulates translation termination by competing with eRF3 for PABP binding, binds pre-mRNA to regulate alternative splicing via spliceosome interactions, and is exploited by SARS-CoV/CoV-2 SUD to selectively enhance viral translation."},"narrative":{"mechanistic_narrative":"PAIP1 is a translational coactivator that enhances cap-dependent translation initiation by bridging the poly(A)-binding protein PABP with the initiation machinery [PMID:11997512, PMID:24396066]. It engages PABP with high affinity (Kd ~1.9 nM) through two independent motifs, an N-terminal PAM2 and a C-terminal acidic PAM1 region, binding PABP's RRM1-2 and C-terminal domain at 1:1 stoichiometry [PMID:11997512]. PAIP1 stimulation of initiation is gated by nutrient signaling: amino acid availability acting through the mTORC1/S6K1/2 axis drives S6K-dependent phosphorylation of eIF3 to promote the PAIP1-eIF3g interaction, and S6K inhibition reduces PAIP1-stimulated translation [PMID:24396066]. Its abundance is controlled by the HECT E3 ligase WWP2, whose WW domain binds the PXXY residues of the PAM2 motif to ubiquitinate PAIP1 and target it for proteasomal degradation [PMID:25266661]. Beyond initiation, PAIP1 modulates translation termination by competing with eRF3 for PABP's C-terminal domain and by directly binding eRF3 [PMID:30992367], and it relieves YBX2-mediated translational repression of spermiogenic mRNAs in testis [PMID:30295753]. PAIP1 additionally functions in mRNA processing, binding GA-rich splicing enhancer motifs in pre-mRNAs and interacting with spliceosome components to regulate alternative splicing of cancer-related transcripts including VEGFA [PMID:39363305]. The SARS-CoV/CoV-2 SUD macrodomain (Mac2) directly binds the middle domain of PAIP1 to selectively enhance viral protein synthesis, a structurally defined interaction [PMID:33876849]. Loss of Paip1 in Drosophila reduces global translation and activates the PERK/eIF2α integrated stress response, driving apoptosis [PMID:37543696].","teleology":[{"year":2002,"claim":"Establishing how PAIP1 physically engages the translation apparatus, this work defined the bipartite, high-affinity architecture of PAIP1-PABP recognition.","evidence":"Far-Western, GST pull-down, and surface plasmon resonance mapping two PABP-binding motifs (PAM1, PAM2) and reciprocal PABP sites","pmids":["11997512"],"confidence":"High","gaps":["Does not establish how this interaction promotes mRNA circularization in vivo","Does not address regulation of the interaction"]},{"year":2014,"claim":"Linked PAIP1 activity to nutrient/growth signaling by showing its eIF3 association is controlled by the mTORC1/S6K pathway.","evidence":"Co-IP, S6K1/2 shRNA knockdown, in vitro kinase assay, and translation assays in cells","pmids":["24396066"],"confidence":"High","gaps":["Exact eIF3 phosphosite(s) required not pinpointed","Quantitative contribution of eIF3g binding to initiation rate unresolved"]},{"year":2014,"claim":"Identified post-translational control of PAIP1 levels, explaining how the cell limits PAIP1-driven translation.","evidence":"Co-IP with domain mapping, ubiquitination assay, proteasome inhibition, and translation readout identifying WWP2 acting on the PAM2 PXXY motifs","pmids":["25266661"],"confidence":"High","gaps":["Signals controlling WWP2 activity toward PAIP1 unknown","Deubiquitinase counteracting WWP2 not identified"]},{"year":2019,"claim":"Extended PAIP1's role from initiation to termination, showing it tunes termination by competing with eRF3 for PABP.","evidence":"In vitro reconstituted translation termination assay and biochemical binding measurements","pmids":["30992367"],"confidence":"High","gaps":["Physiological conditions favoring termination inhibition versus poly(A)-bound activation not defined in cells","Cellular consequences of altered termination unquantified"]},{"year":2019,"claim":"Demonstrated a tissue-specific function by which PAIP1 derepresses stored mRNAs during spermiogenesis.","evidence":"Co-IP, immunofluorescence colocalization, sequential RNA-IP, and in vitro translation rescue of YBX2-repressed mRNAs in murine testes","pmids":["30295753"],"confidence":"Medium","gaps":["In vivo Paip1-loss spermatogenesis phenotype not established","Direct PAIP1-YBX2 interaction interface not mapped"]},{"year":2021,"claim":"Resolved at atomic resolution how a coronaviral protein hijacks PAIP1 to favor viral translation.","evidence":"SEC, split-YFP, Co-IP, X-ray crystallography with SAXS validation, and replicon translation assay of the SARS-CoV SUD-Mac2/Paip1M complex","pmids":["33876849"],"confidence":"High","gaps":["Mechanism by which SUD binding selectively favors viral over host mRNA not fully resolved","Effect on endogenous PAIP1 functions during infection unquantified"]},{"year":2023,"claim":"Established the organismal consequence of PAIP1 loss, connecting it to global translation capacity and stress-induced apoptosis.","evidence":"Drosophila genetic loss-of-function with epistasis, eIF2α phosphorylation, and 5'UTR reporter assays implicating PERK and Xrp1","pmids":["37543696"],"confidence":"Medium","gaps":["Conservation of the ISR/Xrp1 axis in mammals untested","Direct molecular link between Paip1 loss and PERK activation unclear"]},{"year":2024,"claim":"Revealed a nuclear pre-mRNA processing role for PAIP1 beyond cytoplasmic translation, regulating alternative splicing.","evidence":"iRIP-seq, RNA-seq, interactome proteomics, and splicing reporter with GA-motif deletion showing VEGFA exon 6 regulation","pmids":["39363305"],"confidence":"Medium","gaps":["Direct versus indirect splicing regulation not separated","Spliceosomal partner stoichiometry and recruitment mechanism unknown"]},{"year":2024,"claim":"Connected PAIP1 to cancer cell proliferation through control of CCNE2 mRNA stability.","evidence":"RNA-seq, mRNA stability assay after knockdown, western blot, and xenograft in breast cancer cells","pmids":["39259041"],"confidence":"Low","gaps":["No direct PAIP1-CCNE2 mRNA interaction demonstrated","Mechanism linking PAIP1 to transcript stability not defined"]},{"year":null,"claim":"How PAIP1's distinct activities — initiation enhancement, termination modulation, splicing, and mRNA stability — are coordinated and prioritized within a single cell remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified model integrating cytoplasmic translation and nuclear splicing roles","Determinants of transcript-specific selectivity unknown","Mammalian loss-of-function physiology largely uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[8]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[8]}],"complexes":[],"partners":["PABPC1","EIF3G","WWP2","GSPT1","YBX2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H074","full_name":"Polyadenylate-binding protein-interacting protein 1","aliases":[],"length_aa":479,"mass_kda":53.5,"function":"Acts as a coactivator in the regulation of translation initiation of poly(A)-containing mRNAs. Its stimulatory activity on translation is mediated via its action on PABPC1. Competes with PAIP2 for binding to PABPC1. Its association with EIF4A and PABPC1 may potentiate contacts between mRNA termini. May also be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain (Microbial infection) Upon interaction with SARS coronavirus SARS-CoV NSP3 protein, plays an important role in viral protein synthesis","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9H074/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PAIP1","classification":"Not Classified","n_dependent_lines":13,"n_total_lines":1208,"dependency_fraction":0.01076158940397351},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000172239","cell_line_id":"CID000973","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nuclear_membrane","grade":3}],"interactors":[{"gene":"PABPC4","stoichiometry":10.0},{"gene":"GSPT1","stoichiometry":0.2},{"gene":"MIF","stoichiometry":0.2},{"gene":"LARP1","stoichiometry":0.2},{"gene":"PPME1","stoichiometry":0.2},{"gene":"LSM7","stoichiometry":0.2},{"gene":"NSRP1;CCDC55","stoichiometry":0.2},{"gene":"NCOA5","stoichiometry":0.2},{"gene":"PABPC1;PABPC3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000973","total_profiled":1310},"omim":[{"mim_id":"616686","title":"SYNAPTOTAGMIN-BINDING CYTOPLASMIC RNA-INTERACTING PROTEIN; SYNCRIP","url":"https://www.omim.org/entry/616686"},{"mim_id":"611018","title":"POLYADENYLATE-BINDING PROTEIN-INTERACTING PROTEIN 2B; PAIP2B","url":"https://www.omim.org/entry/611018"},{"mim_id":"605604","title":"POLYADENYLATE-BINDING PROTEIN-INTERACTING PROTEIN 2; PAIP2","url":"https://www.omim.org/entry/605604"},{"mim_id":"605184","title":"POLYADENYLATE-BINDING PROTEIN-INTERACTING PROTEIN 1; PAIP1","url":"https://www.omim.org/entry/605184"},{"mim_id":"604679","title":"POLYADENYLATE-BINDING PROTEIN, CYTOPLASMIC, 1; PABPC1","url":"https://www.omim.org/entry/604679"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Plasma membrane","reliability":"Enhanced"},{"location":"Cytosol","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PAIP1"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q9H074","domains":[{"cath_id":"1.25.40.180","chopping":"159-324","consensus_level":"high","plddt":95.0731,"start":159,"end":324},{"cath_id":"-","chopping":"401-434","consensus_level":"medium","plddt":77.8465,"start":401,"end":434}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H074","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H074-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H074-F1-predicted_aligned_error_v6.png","plddt_mean":71.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PAIP1","jax_strain_url":"https://www.jax.org/strain/search?query=PAIP1"},"sequence":{"accession":"Q9H074","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H074.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H074/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H074"}},"corpus_meta":[{"pmid":"11997512","id":"PMC_11997512","title":"Paip1 interacts with poly(A) binding protein through two independent binding motifs.","date":"2002","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11997512","citation_count":125,"is_preprint":false},{"pmid":"33876849","id":"PMC_33876849","title":"The SARS-unique domain (SUD) of SARS-CoV and SARS-CoV-2 interacts with human Paip1 to enhance viral RNA translation.","date":"2021","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/33876849","citation_count":38,"is_preprint":false},{"pmid":"24396066","id":"PMC_24396066","title":"Control of Paip1-eukayrotic translation initiation factor 3 interaction by amino acids through S6 kinase.","date":"2014","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/24396066","citation_count":35,"is_preprint":false},{"pmid":"30992367","id":"PMC_30992367","title":"Polyadenylate-binding protein-interacting proteins PAIP1 and PAIP2 affect translation termination.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30992367","citation_count":27,"is_preprint":false},{"pmid":"25266661","id":"PMC_25266661","title":"Paip1, an effective stimulator of translation initiation, is targeted by WWP2 for ubiquitination and degradation.","date":"2014","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/25266661","citation_count":17,"is_preprint":false},{"pmid":"30731074","id":"PMC_30731074","title":"Role of Paip1 on angiogenesis and invasion in pancreatic cancer.","date":"2019","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/30731074","citation_count":14,"is_preprint":false},{"pmid":"30295753","id":"PMC_30295753","title":"Murine PAIP1 stimulates translation of spermiogenic mRNAs stored by YBX2 via its interaction with YBX2†.","date":"2019","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/30295753","citation_count":13,"is_preprint":false},{"pmid":"31496746","id":"PMC_31496746","title":"Paip1 overexpression is involved in the progression of gastric cancer and predicts shorter survival of diagnosed patients.","date":"2019","source":"OncoTargets and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/31496746","citation_count":13,"is_preprint":false},{"pmid":"38341068","id":"PMC_38341068","title":"YAP1-activated ZNF131 promotes hepatocellular carcinoma cell proliferation through transcriptional regulation of PAIP1.","date":"2024","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/38341068","citation_count":6,"is_preprint":false},{"pmid":"37543696","id":"PMC_37543696","title":"Loss of Paip1 causes translation reduction and induces apoptotic cell death through ISR activation and Xrp1.","date":"2023","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/37543696","citation_count":6,"is_preprint":false},{"pmid":"34277791","id":"PMC_34277791","title":"Upregulation of PAIP1 promotes the gallbladder tumorigenesis through regulating PLK1 level.","date":"2021","source":"Annals of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34277791","citation_count":5,"is_preprint":false},{"pmid":"37101794","id":"PMC_37101794","title":"PAIP1 regulates expression of immune and inflammatory response associated genes at transcript level in liver cancer cell.","date":"2023","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/37101794","citation_count":3,"is_preprint":false},{"pmid":"35378711","id":"PMC_35378711","title":"Circ_0005576 Exerts an Oncogenic Role in Cervical Cancer via miR-1305-Dependent Regulation of PAIP1.","date":"2022","source":"Reproductive sciences (Thousand Oaks, Calif.)","url":"https://pubmed.ncbi.nlm.nih.gov/35378711","citation_count":3,"is_preprint":false},{"pmid":"39363305","id":"PMC_39363305","title":"PAIP1 binds to pre-mRNA and regulates alternative splicing of cancer pathway genes including VEGFA.","date":"2024","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/39363305","citation_count":2,"is_preprint":false},{"pmid":"36436074","id":"PMC_36436074","title":"PAIP1 is a novel oncogene in human hepatocellular carcinoma.","date":"2022","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/36436074","citation_count":2,"is_preprint":false},{"pmid":"19851022","id":"PMC_19851022","title":"Crystallization and preliminary X-ray diffraction analysis of the middle domain of Paip1.","date":"2009","source":"Acta crystallographica. Section F, Structural biology and crystallization communications","url":"https://pubmed.ncbi.nlm.nih.gov/19851022","citation_count":2,"is_preprint":false},{"pmid":"39259041","id":"PMC_39259041","title":"Knockdown of PAIP1 Inhibits Breast Cancer Cell Proliferation by Regulating Cyclin E2 mRNA Stability.","date":"2024","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/39259041","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10064,"output_tokens":2596,"usd":0.034566,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9750,"output_tokens":3152,"usd":0.063775,"stage2_stop_reason":"end_turn"},"total_usd":0.098341,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2002,\n      \"finding\": \"Paip1 contains two independent PABP-binding motifs: PAM2 (a 15-amino-acid stretch in the N-terminus) and PAM1 (a larger C-terminal acidic-amino-acid-rich region). PABP reciprocally contains two Paip1-binding sites: one in RNA recognition motifs 1 and 2, and one in its C-terminal domain. Paip1 binds PABP with 1:1 stoichiometry and an apparent Kd of 1.9 nM.\",\n      \"method\": \"Far-Western, GST pull-down, and surface plasmon resonance assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal in vitro binding assays (far-Western, GST pulldown, SPR) with quantitative affinity measurement; single lab but three independent methods\",\n      \"pmids\": [\"11997512\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Paip1 interacts with the eIF3g subunit of eIF3, and this interaction is regulated by amino acids through the mTORC1/S6K1/2 signaling pathway. S6K1/2 phosphorylate eIF3 to promote Paip1-eIF3 interaction, enhancing translation initiation. Rapamycin, PP242, and S6K inhibitors impair the Paip1-eIF3 interaction, and S6K inhibition reduces Paip1-stimulated translation.\",\n      \"method\": \"Co-immunoprecipitation, shRNA knockdown of S6K1/2, in vitro phosphorylation assay, translation assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP, in vitro kinase assay, genetic (shRNA) perturbation, and functional translation readout; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"24396066\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The HECT-type E3 ubiquitin ligase WWP2 interacts with Paip1 via its WW domain binding to the PAM2 motif (specifically the two consecutive PXXY motifs) of Paip1, targeting Paip1 for ubiquitination and proteasomal degradation, thereby reducing Paip1-stimulated translation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, domain mapping, proteasome inhibitor treatment, translation assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping, functional ubiquitination assay, and translation readout; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"25266661\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PAIP1 and PAIP2 inhibit PABP-dependent translation termination by competing with eRF3 for binding to the C-terminal domain of PABP. PAIP1 also directly binds eRF3 in solution, which stabilizes the post-termination complex. When PABP is bound to the poly(A) tail, it becomes insensitive to PAIPs and efficiently activates translation termination.\",\n      \"method\": \"In vitro translation termination assay, biochemical binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstituted translation termination assay with direct binding measurements; single lab, multiple assay conditions\",\n      \"pmids\": [\"30992367\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PAIP1 interacts with YBX2 in vitro and in vivo in murine testes, and PAIP1 co-localizes with YBX2 in round spermatids. PAIP1 relieves YBX2-mediated translational repression of spermiogenic mRNAs bearing the YBX2 target sequence, as demonstrated by sequential RNA immunoprecipitation and in vitro translation assays.\",\n      \"method\": \"Co-immunoprecipitation, colocalization (immunofluorescence), sequential RNA immunoprecipitation, in vitro translation assay\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and functional in vitro translation rescue; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"30295753\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The SARS-CoV SUD (macrodomain II, Mac2) directly interacts with the middle domain of Paip1, and the crystal structure of this complex was determined by X-ray crystallography and validated by small-angle X-ray scattering. This interaction is conserved with SARS-CoV-2. SUD enhances viral (but not host) protein synthesis via Paip1 binding in replicon-transfected cells.\",\n      \"method\": \"Size-exclusion chromatography, split-YFP, co-immunoprecipitation, X-ray crystallography, small-angle X-ray scattering, replicon translation assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with SAXS validation, multiple binding assays (SEC, split-YFP, Co-IP), and functional in cellulo translation readout; single lab but multiple highly rigorous orthogonal methods\",\n      \"pmids\": [\"33876849\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In Drosophila, loss of Paip1 causes reduced protein translation, activates the integrated stress response (ISR) via PERK-mediated eIF2α phosphorylation, and leads to apoptotic cell death. Loss of Paip1 also upregulates the transcription factor Xrp1, whose translation is enhanced via its 5'UTR, and Xrp1 in turn contributes to eIF2α phosphorylation and apoptosis.\",\n      \"method\": \"Genetic loss-of-function (Drosophila knockdown/knockout), epistasis analysis, eIF2α phosphorylation assay, 5'UTR reporter assay\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis in Drosophila model organism with multiple downstream pathway readouts; single lab\",\n      \"pmids\": [\"37543696\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The middle domain of Paip1 (Paip1M) was crystallized and produced diffraction data to 2.2 Å resolution, providing structural information on this domain.\",\n      \"method\": \"X-ray crystallography (preliminary diffraction analysis)\",\n      \"journal\": \"Acta crystallographica. Section F\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 / Weak — preliminary crystallographic data only, no functional validation reported in this communication\",\n      \"pmids\": [\"19851022\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PAIP1 binds directly to pre-mRNAs/mRNAs with enrichment at coding regions and introns (GA-rich splicing enhancer motifs), interacts with spliceosome components and splicing factors (by proteomics), and regulates alternative splicing of cancer-related genes including VEGFA. Deletion of a PAIP1-binding GA-repeat motif reduced PAIP1-mediated suppression of VEGFA exon 6 inclusion.\",\n      \"method\": \"iRIP-seq (UV cross-linking RNA immunoprecipitation sequencing), RNA-seq, proteomic analysis of PAIP1-interacting proteins, splicing reporter with binding-site deletion\",\n      \"journal\": \"BMC genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — iRIP-seq with RNA-seq and functional splicing reporter mutagenesis; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"39363305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PAIP1 knockdown in breast cancer cells reduces cyclin E2 (CCNE2) expression by decreasing the mRNA stability of CCNE2, leading to cell cycle arrest and inhibition of proliferation.\",\n      \"method\": \"RNA-seq, mRNA stability assay (knockdown), western blot, xenograft model\",\n      \"journal\": \"Molecular carcinogenesis\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mRNA stability assay without direct mechanistic demonstration of PAIP1-CCNE2 mRNA interaction\",\n      \"pmids\": [\"39259041\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PAIP1 is a translation stimulator that binds PABP via two independent motifs (PAM1 and PAM2) and also interacts with eIF3 (via eIF3g) in an mTORC1/S6K-regulated manner to enhance cap-dependent translation initiation through mRNA circularization; its activity is negatively regulated by WWP2-mediated ubiquitination and proteasomal degradation; it also modulates translation termination by competing with eRF3 for PABP binding, binds pre-mRNA to regulate alternative splicing via spliceosome interactions, and is exploited by SARS-CoV/CoV-2 SUD to selectively enhance viral translation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PAIP1 is a translational coactivator that enhances cap-dependent translation initiation by bridging the poly(A)-binding protein PABP with the initiation machinery [#0, #1]. It engages PABP with high affinity (Kd ~1.9 nM) through two independent motifs, an N-terminal PAM2 and a C-terminal acidic PAM1 region, binding PABP's RRM1-2 and C-terminal domain at 1:1 stoichiometry [#0]. PAIP1 stimulation of initiation is gated by nutrient signaling: amino acid availability acting through the mTORC1/S6K1/2 axis drives S6K-dependent phosphorylation of eIF3 to promote the PAIP1-eIF3g interaction, and S6K inhibition reduces PAIP1-stimulated translation [#1]. Its abundance is controlled by the HECT E3 ligase WWP2, whose WW domain binds the PXXY residues of the PAM2 motif to ubiquitinate PAIP1 and target it for proteasomal degradation [#2]. Beyond initiation, PAIP1 modulates translation termination by competing with eRF3 for PABP's C-terminal domain and by directly binding eRF3 [#3], and it relieves YBX2-mediated translational repression of spermiogenic mRNAs in testis [#4]. PAIP1 additionally functions in mRNA processing, binding GA-rich splicing enhancer motifs in pre-mRNAs and interacting with spliceosome components to regulate alternative splicing of cancer-related transcripts including VEGFA [#8]. The SARS-CoV/CoV-2 SUD macrodomain (Mac2) directly binds the middle domain of PAIP1 to selectively enhance viral protein synthesis, a structurally defined interaction [#5]. Loss of Paip1 in Drosophila reduces global translation and activates the PERK/eIF2\\u03b1 integrated stress response, driving apoptosis [#6].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Establishing how PAIP1 physically engages the translation apparatus, this work defined the bipartite, high-affinity architecture of PAIP1-PABP recognition.\",\n      \"evidence\": \"Far-Western, GST pull-down, and surface plasmon resonance mapping two PABP-binding motifs (PAM1, PAM2) and reciprocal PABP sites\",\n      \"pmids\": [\"11997512\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not establish how this interaction promotes mRNA circularization in vivo\", \"Does not address regulation of the interaction\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked PAIP1 activity to nutrient/growth signaling by showing its eIF3 association is controlled by the mTORC1/S6K pathway.\",\n      \"evidence\": \"Co-IP, S6K1/2 shRNA knockdown, in vitro kinase assay, and translation assays in cells\",\n      \"pmids\": [\"24396066\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Exact eIF3 phosphosite(s) required not pinpointed\", \"Quantitative contribution of eIF3g binding to initiation rate unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified post-translational control of PAIP1 levels, explaining how the cell limits PAIP1-driven translation.\",\n      \"evidence\": \"Co-IP with domain mapping, ubiquitination assay, proteasome inhibition, and translation readout identifying WWP2 acting on the PAM2 PXXY motifs\",\n      \"pmids\": [\"25266661\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signals controlling WWP2 activity toward PAIP1 unknown\", \"Deubiquitinase counteracting WWP2 not identified\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended PAIP1's role from initiation to termination, showing it tunes termination by competing with eRF3 for PABP.\",\n      \"evidence\": \"In vitro reconstituted translation termination assay and biochemical binding measurements\",\n      \"pmids\": [\"30992367\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological conditions favoring termination inhibition versus poly(A)-bound activation not defined in cells\", \"Cellular consequences of altered termination unquantified\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrated a tissue-specific function by which PAIP1 derepresses stored mRNAs during spermiogenesis.\",\n      \"evidence\": \"Co-IP, immunofluorescence colocalization, sequential RNA-IP, and in vitro translation rescue of YBX2-repressed mRNAs in murine testes\",\n      \"pmids\": [\"30295753\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo Paip1-loss spermatogenesis phenotype not established\", \"Direct PAIP1-YBX2 interaction interface not mapped\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Resolved at atomic resolution how a coronaviral protein hijacks PAIP1 to favor viral translation.\",\n      \"evidence\": \"SEC, split-YFP, Co-IP, X-ray crystallography with SAXS validation, and replicon translation assay of the SARS-CoV SUD-Mac2/Paip1M complex\",\n      \"pmids\": [\"33876849\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which SUD binding selectively favors viral over host mRNA not fully resolved\", \"Effect on endogenous PAIP1 functions during infection unquantified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Established the organismal consequence of PAIP1 loss, connecting it to global translation capacity and stress-induced apoptosis.\",\n      \"evidence\": \"Drosophila genetic loss-of-function with epistasis, eIF2\\u03b1 phosphorylation, and 5'UTR reporter assays implicating PERK and Xrp1\",\n      \"pmids\": [\"37543696\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Conservation of the ISR/Xrp1 axis in mammals untested\", \"Direct molecular link between Paip1 loss and PERK activation unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealed a nuclear pre-mRNA processing role for PAIP1 beyond cytoplasmic translation, regulating alternative splicing.\",\n      \"evidence\": \"iRIP-seq, RNA-seq, interactome proteomics, and splicing reporter with GA-motif deletion showing VEGFA exon 6 regulation\",\n      \"pmids\": [\"39363305\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect splicing regulation not separated\", \"Spliceosomal partner stoichiometry and recruitment mechanism unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected PAIP1 to cancer cell proliferation through control of CCNE2 mRNA stability.\",\n      \"evidence\": \"RNA-seq, mRNA stability assay after knockdown, western blot, and xenograft in breast cancer cells\",\n      \"pmids\": [\"39259041\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct PAIP1-CCNE2 mRNA interaction demonstrated\", \"Mechanism linking PAIP1 to transcript stability not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PAIP1's distinct activities — initiation enhancement, termination modulation, splicing, and mRNA stability — are coordinated and prioritized within a single cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified model integrating cytoplasmic translation and nuclear splicing roles\", \"Determinants of transcript-specific selectivity unknown\", \"Mammalian loss-of-function physiology largely uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-72766\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PABPC1\", \"EIF3G\", \"WWP2\", \"GSPT1\", \"YBX2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}