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Heller"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["nvs1.1","Usp9x","ubiquitination","rqc","erf1","ternatin-4","Usp9x; rqc; ribosome collisions; erf1; proteasomal degradation; eef1a1; ubiquitination; nvs1.1; ternatin-4","ribosome collisions","eef1a1","proteasomal degradation"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD079916"],"tissue":["Embryonic Kidney Cell Line","Hek-293 Cell"],"sample_protocol":["Global proteome analysis by label-free mass spectrometry: For global proteome analysis following polysome fractionation, fractions corresponding to disomes or heavy polysomes were combined with one volume of acetone and 0.1 volumes of 100% trichloroacetic acid (TCA). Samples were incubated overnight at −80 °C to precipitate proteins, which were subsequently pelleted by centrifugation at 16,000 × g for 5 minutes at 4 °C. The resulting pellets were washed three times with ice-cold acetone, with centrifugation performed under the same conditions after each wash. Heavy polysome fractions were pooled, and both heavy polysome and disome samples were dried for 20 minutes in a SpeedVac concentrator before storage at −80°C. Protein pellets were resuspended in 12 µL of lysis buffer containing 8 M urea and 100 mM Tris-HCl (pH 8). Protein concentration was determined using 2 µL diluted ten times in water using the Qubit Protein Assay (Invitrogen, Cat# Q33211). The remaining sample was reduced and alkylated as described elsewhere [1].  DiGly (K-ε-GG) ubiquitin remnant analysis: DiGly proteomics was performed using HEK293 cells expressing either catalytically active USP9X (USP9X_SILENT) or a catalytically dead mutant (USP9X_CD). Cells were treated with 25 μM NVS1.1 for 6 h, harvested by scraping, and collected by centrifugation. Cell pellets were lysed in 8 M urea, 150 mM NaCl, and 50 mM Tris-HCl (pH 8.0) supplemented with 5 mM N-ethylmaleimide (MedChemExpress, Cat# HY-D0843), complete protease inhibitor cocktail (TargetMol, Cat# C0001), and phosphatase inhibitor cocktails (TargetMol, Cat# C0002 and C0003). Samples were homogenized by centrifugation in a Zentrimix 380R (Hettich, Cat# 3220) at 1,500 rpm for 4 minutes at 5°C. Lysates were subsequently cleared by centrifugation at 13,000 × g for 10 minutes at 4°C, and total protein concentration was determined using Direct Detect® (Merck, Cat# DDHW00010-WW). A total of 1 mg of protein per sample was subjected to overnight digestion with trypsin (Promega, Cat# V5111) according to a previously described protocol [2]. Ubiquitin remnant-containing peptides were enriched using Ubiquitin Remnant (K-ε-GG) Immunoaffinity Beads (Cayman, Cat# 34699) according to the manufacturer’s instructions. Briefly, lyophilized peptides were dissolved in 1 mL ice-cold Immunoaffinity Purification (IAP) buffer (50 mM MOPS, pH 7.2, 10 mM disodium phosphate, 50 mM NaCl) and vortexed. The peptide supernatant was added to tubes containing immunoaffinity beads (30 µL bead volume) pre-washed four times with 1 mL of cold IAP buffer. Samples were rotated for 1 hour at 4°C, after which the supernatant was removed. Beads were washed three times with 1 mL ice-cold IAP buffer and three times with 1 mL ice-cold HPLC-grade water. Peptides were eluted by two consecutive incubations with 50 µL 0.1% trifluoroacetic acid (TFA) for 10 minutes at room temperature with gentle agitation every 2–3 minutes. Eluates were dried by vacuum concentration and stored at −80°C until analysis.   eRF1 ubiquitin remnant analysis: HEK293 cells expressing either catalytically active USP9X (USP9X_SILENT) or a catalytically dead mutant (USP9X_CD) were treated with 25 μM NVS1.1 for 1 h, washed with ice-cold PBS, and harvested by scraping. Pellets were lysed in IP buffer (50 mM HEPES, pH 7.3; 600 mM NaCl; 0.5% Triton X-100) and homogenized by centrifugation in a Zentrimix 380R (Hettich, Cat# 3220) at 1,500 rpm for 4 minutes at 5°C. Lysates were cleared by centrifugation at 13,000 × g for 10 minutes at 4°C, and total protein was quantified using Direct Detect® (Merck, Cat# DDHW00010-WW) and normalized to equal protein concentrations across samples. Lysates were incubated with 6 μg eRF1 antibody (Santa Cruz Biotechnology, Cat# sc-365686) pre-bound to 0.75 mg Dynabeads Protein G (Invitrogen, Cat# 10004D) for 1 hour at 4°C with rotation. Beads were washed three times with IP buffer and three times with HPLC-grade water. After immunoprecipitations, proteins associated with the Dynabeads were resuspended in 8 M urea, 50 mM Tris-HCl pH 8, reduced at 37°C for 30 min with 0.1 M DTT, 50 mM Tris-HCl pH 8, alkylated at 37°C for 30 min in the dark with 0.5 M iodoacetamide (IAA), 50 mM Tris-HCl pH 8, diluted with 4 volumes of 20 mM Tris-HCl pH 8 2 mM CaCl2 prior to two hour digestion with a mix of 50 ng LysC and 100 ng trypsin (sequencing grade, Promega, Switzerland) at 37°C. Samples were then centrifuged, the magnetic beads were trapped by a magnet, and the peptide-containing supernatant was collected.  REF:  1 Braga-Lagache S et al (2016) Robust Label-Free. Mol Cell Proteomics. 15: 3640-3652. doi: 10.1074/mcp.M116.060491 2.Oltion, K. et al (2023). Cell 186, 346-362.e17. https://doi.org/10.1016/j.cell.2022.12.025."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Global proteome analysis: Each sample was analysed twice by loading 500 ng digested proteins onto a pre-column (C18 PepMap 100, 5µm, 100A, 300µm i.d. x 5mm length) at a flow rate of 10µL/min with 0.05% TFA in water/acetonitrile 98:2 with an Ultimate 3000 nano-UPLC (Thermo Fischer, Bremen; Germany). After loading, peptides were eluted in back flush mode onto a homemade C18 CSH Waters column (1.7 μm, 130 Å, 75 μm × 20 cm) by applying a 90-minute gradient of 5% acetonitrile to 40% in water, 0.1% formic acid, at a flow rate of 250 nl/min. The column effluent was directly coupled to a Fusion LUMOS mass spectrometer (Thermo Fischer, Bremen; Germany) via a nano-spray ESI source. Data acquisition was made in data dependent mode with precursor ion scans recorded in the orbitrap with resolution of 120’000 (at m/z=250) parallel to top speed fragment spectra of the most intense precursor ions in the Linear trap for a cycle time of 3 seconds maximum. Protein identification and quantification were performed using FragPipe version 20.0. Database searches were conducted against the SwissProt human reference proteome (issue April 2023) including isoforms and common contaminants. Precursor and fragment mass tolerances were set to 20 ppm and 0.4 Da, respectively. Searches were performed using trypsin specificity with up to three missed cleavages permitted. Carbamidomethylation of cysteine residues was specified as a fixed modification, whereas methionine oxidation, lysine diglycine modification, and protein N-terminal acetylation were included as variable modifications. Peptide validation and protein inference were carried out using PeptideProphet and ProteinProphet within the Philosopher framework, while quantitative analysis was performed with IonQuant. PTMprophet was enabled with minimum localization probability of 0.5. Match-between-runs functionality was enabled, using a maximum of 5 top runs.    DiGly (K-ε-GG) ubiquitin remnant: Peptides were reconstituted in 5% formic acid at a concentration of 130 ng/µL and analysed on a timsTOF HT (Bruker Daltonics, Bremen, Germany), with an Ultimate 3000 nano-UPLC (Thermo Fischer, Bremen; Germany) coupled through a CaptiveSpray source (Bruker, Bremen, Germany) with an end-plate offset of 500 V, a drying temperature of 200 °C, and with the capillary voltage fixed at 1.6 kV. A volume of 2 µL from the enriched peptides were loaded onto a C18-Saphir trap column (5x0.3 mm, Dr. Maisch, Germany) then chromatographically analysed like described above applying a 30-min active acetonitrile gradient. Data were acquired in data-dependant (DDA) and independent (DIA) acquisition mode. For DDA eight PASEF ramps with an ion mobility range from 0.75 to 1.35 1/k0, in the m/z range between 100–1700 u and a cycle time of 0.95 s at an acquisition rate of 300Hz were employed. For DIA 32 isolation windows were set, each 26 m/z wide, with a 1 m/z overlap between adjacent windows. These isolation windows corresponded to an ion mobility range of 0.75–1.36 V s/cm². Both TIMS accumulation and separation times were set at 100 ms. Samples were analysed in the DIA + DDA hybrid mode by Spectronaut version 20.5.260227.92449 against the human SwissProt proteome [6](issue January 2026) plus common contaminants. Precursor and fragment mass tolerances were set to 20 ppm and 0.05 Da, respectively. Cleavage rule was set to trypsin, with a maximum of two missed cleavages. Fixed modification was Carbamidomethylation of cysteine; variable modifications were methionine oxidation,lysine diglycine and ubiquitination modification, and protein N-terminal acetylation. The cutoff of precursor and protein qvalue and PEP was set to 0.01.   eRF1 ubiquitin remnant: An aliquote of 4 µL of the digested 213 samples were analysed on nanoElute 2 UPLC coupled to a timsTOF HT (Bruker, Bremen, Germany) employing only the DDA method and a PepSepC18 analytical column (1.5 Å, 150 μm × 15 cm, Bruker, Germany) as described for the DiGly ubiquitin remnant study. Identification and quantification was performed using FragPipe version 24.0 [3-5], against the SwissProt human reference proteome (issue January 2026) including isoforms and common contaminants. Precursor and fragment mass tolerances were set to 20 ppm and 0.4 Da, respectively. Searches were performed using trypsin specificity with up to three missed cleavages permitted. Allowed modifications were the same as for the DiGly ubiquitin remnant study. Peptide validation and protein inference were carried out using percolator and ProteinProphet within the Philosopher framework, with Msbooster (models: rt model Prosit_2024_irt_cit, spectral model Prosit_2023_intensity_timsTOF). PTMprophet was enabled with minimum localization probability of 0.75.  Match-between-runs functionality was enabled, using a maximum of two top runs."],"omics_type":["Proteomics"],"labhead":["Oliver Mühlemann"],"instrument_platform":[""],"labhead_affiliation":["Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["pmscf.dbmr@unibe.ch"],"publication":["Not available"],"submitter_affiliation":["Proteomics and Mass Spectrometry Core Facility,\nDepartement for Biomedical Research,\nUniversity of Berne"],"submitter_country":["Switzerland"],"additional_accession":[]},"is_claimable":false,"name":"USP9X promotes the degradation of trapped translation factors on collided ribosomes","description":"Various ribosome-associated quality control pathways safeguard translation fidelity by detecting and resolving aberrant translation events. Recently, a pathway that senses stalled ribosomes with an occluded A-site has been described. The small molecules NVS1.1 and Ternatin-4 induce ribosome stalling by trapping eRF1 and eEF1A1, respectively, within the ribosomal A-site, thereby promoting their ubiquitination and proteasomal degradation. Here, in addition to the previously identified factors GCN1, RNF14, and RNF25, we identify the deubiquitinase USP9X as a regulator of this pathway. USP9X is required for efficient clearance of A-site–trapped proteins and regulates K6-linked ubiquitination of eRF1, a modification associated with VCP-dependent substrate processing. In the absence of USP9X activity, K6-linked ubiquitinated eRF1 accumulates, suggesting defective ubiquitin-chain remodeling and impaired downstream degradation. Furthermore, clearance of trapped translation factors engages a feedback mechanism involving 4EHP and the integrated stress response (ISR) to suppress translation, whereas impaired degradation prevents efficient translational shutdown.","dates":{"publication":"2026-09-22","submission":"2026-06-19"},"accession":"PXD079916","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:309807","NEWT:55153","NEWT:10244","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:43186","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:641809","NEWT:27933","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:79329","NEWT:4442","NEWT:31155","NEWT:192875","NEWT:1214915","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:60711","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:160621","NEWT:212790","NEWT:931281","NEWT:4432","NEWT:5762","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NEWT:2246","NEWT:2652724","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:1367269","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:4897","NEWT:1148","NEWT:5744","NEWT:5508","NEWT:3329","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1235816","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:2065263","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:1246791","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:7070","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:9483","NEWT:333760","NEWT:1513458","NEWT:1233681","NCBITaxon:40559","NEWT:506599","NEWT:2853422","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:65349","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:109760","NEWT:943274","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:5936","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:2719099","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:55529","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1116234","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:352472","NEWT:1071661","NEWT:1202532","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:1218097","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:153009","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:215402","NCBITaxon:548681","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:1034015","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:8694","NEWT:4093","NEWT:4096","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:941442","NEWT:536088","NEWT:13076","NEWT:1226408","NEWT:7108","NEWT:40479","NEWT:43989","NEWT:4076","NEWT:142615","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:552","NEWT:4084","NEWT:63577","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8655","NEWT:98351","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:207559","NEWT:407821","NCBITaxon:2","NEWT:85057","NEWT:985076","NEWT:568708","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:267671","NEWT:28532","NEWT:198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