{"database":"JPOST Repository","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["https://storage.jpostdb.org/JPST001320/files/201005_Yasuda_siRad23B_TMT16_bRP9_re.xlsx"],"Raw":["https://storage.jpostdb.org/JPST001320/files/235_Yasuda_siRad23B_TMT16_bRP9_8re.raw","https://storage.jpostdb.org/JPST001320/files/233_Yasuda_siRad23B_TMT16_bRP9_7re.raw","https://storage.jpostdb.org/JPST001320/files/223_Yasuda_siRad23B_TMT16_bRP9_2re.raw","https://storage.jpostdb.org/JPST001320/files/229_Yasuda_siRad23B_TMT16_bRP9_5re.raw","https://storage.jpostdb.org/JPST001320/files/225_Yasuda_siRad23B_TMT16_bRP9_3re.raw","https://storage.jpostdb.org/JPST001320/files/227_Yasuda_siRad23B_TMT16_bRP9_4re.raw","https://storage.jpostdb.org/JPST001320/files/231_Yasuda_siRad23B_TMT16_bRP9_6re.raw","https://storage.jpostdb.org/JPST001320/files/237_Yasuda_siRad23B_TMT16_bRP9_9re.raw"],"Other":["https://storage.jpostdb.org/JPST001320/files/201005_Yasuda_siRad23B_TMT16_bRP9_re.pdResult"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Hidetaka Kosako"],"species":["Homo Sapiens (human)"],"full_dataset_link":["https://repository.jpostdb.org/entry/JPST001320"],"submitter_affiliation":["Tokushima University"],"sample_protocol":[""],"repository":["jPOST"],"data_protocol":[""],"pubmed_abstract":["The proteasome plays a central role in intracellular protein degradation. Age-dependent decline in proteasome activity is associated with cellular senescence and organismal aging; however, the mechanism by which the proteasome plays a role in senescent cells remains elusive. Here, we show that nuclear foci that contain the proteasome and exhibit liquid-like properties are formed in senescent cells. The formation of senescence-associated nuclear proteasome foci (SANPs) is dependent on ubiquitination and RAD23B, similar to previously known nuclear proteasome foci, but also requires proteasome activity. RAD23B knockdown suppresses SANP formation and increases mitochondrial activity, leading to reactive oxygen species production without affecting other senescence traits such as cell-cycle arrest and cell morphology. These findings suggest that SANPs are an important feature of senescent cells and uncover a mechanism by which the proteasome plays a role in senescent cells."],"pubmed_title":["Senescent cells form nuclear foci that contain the 26S proteasome."],"pubmed_authors":["Iriki Tomohiro T, Iio Hiroaki H, Yasuda Shu S, Masuta Shun S, Kato Masakazu M, Kosako Hidetaka H, Hirayama Shoshiro S, Endo Akinori A, Ohtake Fumiaki F, Kamiya Mako M, Urano Yasuteru Y, Saeki Yasushi Y, Hamazaki Jun J, Murata Shigeo S"],"name_synonyms":["ETP, PlexB, determination, PlexA, ethionamidum, etionamida, plex A, Etioniamid, plex B, Ethyonomide, Ethioniamide, Ethinamide, CG11081, Ethylisothiamide, preT.ETP.Th, plex, Plex1, CG17245, DmelCG17245, 2-ethyl-4-thiopyridylamide, DmelCG11081, DPlexA, chemical analysis, Etionamid, Trecator, Cell., D-Plex A, assay, ETH, PLEXB, Etionamide, PlexA1, BcDNA:GM05237"],"pubmed_abstract_synonyms":["F20B17.8, d230, nucleocytoplasm, cycline, Activity, Cell Aging, FESTA-L, FESTA-S, Feature, RADIATION SENSITIVE23B, DmcyclinE, fond, Degradation, p58, Reactive Oxygen Intermediates, dTAFII250, cycE, Cellular Aging, Aging, CycEI, mitochondrial, EfW1, l(2)br37, CYCLE, cdi7, dmTAF[[II]]230, cellular structure, Multicatalytic Proteinase, Ccne, cyclinE, Roles, dmTAF1, Multicatalytic Endopeptidase Complex, Biological, Taf230, 0610007D13Rik, Cdi7, CDI7, symptoms, Concepts, AW048865, Cell., F20B17_8, Pro Oxidant, Reactive, U19, Cell Ageing, multicellular organismal biosynthetic process, TAF250, protoplasm, Senescence, single-organism biosynthetic process, BM040, Taf200, Ubiquitylation, pheromone catabolism, dTAF[[II]]250, CYCE, protoplast, TFIID TAF250, ATP-dependent proteolysis, Macropain, cel, Replicative Senescence, cell, DmelCG3938, CyclE, Complex, 3938, RAD23, Taf1p, DmcycE, Protein Degradations, Proteasome Endopeptidase, 20S Proteasome, Protein Degradation, Oxygen Species, Cell Senescence, l(2)k05007, Oxygen, dTAF250, Biological Aging, dm-cycE, Ageing, Multicatalytic Endopeptidase, Replicative, Active Oxygen Species, Multicatalytic, Role Concepts, Macroxyproteinase, 26S proteasome, liquid, ubiquitination, Characteristics, HHR23B, Pro-Oxidant, associated, TAF, Active Oxygen, screening, dTAF[[II]]230, TAF[[II]]250, Proteinase, Degradations, Pro Oxidants, Endopeptidase Complex, findings, RnBP, Traits, Oxygen Radical, Cellular Ageing, TAF200, GlcNAc 2-epimerase, l(3)84Ab, mHR23B, BG:DS00004.13, TAFII-250, Protein Digestion, TAF250/230, Cyc E, br37, cell structure, Digestions, Cell, Proteasome, cellular morphology, Concept, dTAF230, Ingensin, N-acetyl-D-glucosamine 2-epimerase, TAFII250, cellular aspects, Role Concept, l(2)k02514, Characteristic, DmCycE, BG:DS07108.3, Proteolyses, ATP synthase D chain, Digestion, p230, RENBP, Protein, Role, TAF[[II]]250/230, Cellular, Active, TFIID, CyeE, internal to cell, l(2)05206, Oxygen Radicals, proteasome, Taf[[II]]250, pheromone catabolic process, Mitochondrial, Exhibit, TAF[[II]]230, l(2)k02602, HR23B, Prosome, Radical, Protein Digestions, l(2)35Dd, AV001138, signs, 20S, TAF[II]250, CG17603, Features, TAF[[II]], TRAITS, AGE, D-CycE, DmelCG17603, l35Dd, Taf250, Festa, SR3-5, Pro-Oxidants, renin-binding protein, P58, multicatalytic endopeptidase, CG3938, General activity, cell morphology, TAF230, proteasome endopeptidase complex, TAF1"],"pubmed_title_synonyms":["Forms, proteasome, 26S proteasome, 26S protease, 26 S proteasome complex., Cell"],"description_synonyms":["Methane, Raw, ion, Lysine Hydrochloride, chronic obstructive pulmonary disease (COPD), Ethylisothiamide, prevention, trichloro-, Long Term, nodus primitivus., 5730420M11Rik, Repeat Associated siRNA, Small, Polypeptides, DmelCG11081, KL receptor activity, Lysine Acetate, hydrogen chloride, T22F8_160, dorsal marginal zone, Method, ATGPR7, DPlexA, Etionamid, B1, Post Transcriptional, Chronic irreversible airway obstruction, SCO5, GRP8, 2, GRP7, SCO1, Gsfsow3, WMS, L Lysine, SET, Divorced, C79325, ethionamidum, K, M, Salt, RAD23, CAFL - Chronic airflow limitation, Divorces, W, T6G21.3, CG17245, AI047805, DmelCG4299, isolation and purification, Gene Silencings, set, Wasserstoffchlorid, LYS, Repeat-Associated, column, disease (COPD), ACN, Lysin, sample, Acn, D1, Bs, Half Cystine, SGS, LC-MS2, chronic obstructive lung disease [Ambiguous], preventive therapy, Stars, BZRP, Zinc Cysteinate, Trypsin/K, Longterm Effect, Ethinamide, Guanidine Monohydroiodine, Procedure, LF2000, Short, PBS, ACMICD, PBR, CHRONIC OBSTRUCTIVE AIRWAY DIS, PBT, TPSG1, Dm1, Chlorwasserstoff, Methionin, Hmet, Airflow Obstruction, BcDNA:GM05237, Post-Transcriptional Gene, GLYCINE-RICH PROTEIN 8, Chronic Obstructive Airways Disease, Chronic obstructive lung disease, pbt, HLA-DR-associated protein II, DI-2, HR23B, I-2Dm, AV001138, Guanidine Phosphate, Methodological, alpha, Repeat Associated, sodium hydrate, Co Suppression, beta Trypsin, human, Post Transcriptional Gene Silencing, I-2PP1, Gene Silencing, Painful bladder syndrome, TAF-IBETA, F2G1.4, OBSTRUCTIVE PULMONARY DISEASE (COPD), spirit of wood, liquid chromatography-tandem mass spectroscopy, Indicator, PRSS31, DMZ, TAF-Ibeta, chlorane, STARS, TMT, Liquimeth, glutamic acid side-chain, Methyl Alcohol, krk1, BPBS, post-transcriptional gene silencing by RNA, F20B17.8, 2-amino-4-(methylsulfanyl)butanoic acid, Effects, chlorure d'hydrogene, Biocatalysts, CAO - Chronic airflow obstruction, Pierce, CH3OH, CHRONIC OBSTRUCTIVE PULM DIS, preT.ETP.Th, precursor, Chronic obstructive pulmonary disease NOS, abdominal muscles, thomson, 17alpha)-isomer, and RNA binding 1, CG7826, mass-to-charge ratio, Human, Chronic obstructive pulmonary disease finding, PULMONARY DISEASE (COPD), Guanidium, isolation, 0610007D13Rik, Small Scan RNA, LC-MSMS, CG7835, Gene Products, CG42273, Lysine, Half-Cystine, PH3, Technique, Man, scnRNA, Monohydroiodine, Acinus, Hydrogen chloride, Longterm, nodus primitivus, L Cysteine, plex A, Monosodium Salt, beta-Trypsin, plex B, 2pp2a, pk18, Long-Term, ions, Cosuppression, man, MBR, CG10574, Short Hairpin, DmelCG17245, acinusL, Study, Injectable, Enzyme, Monohydrobromide, Guanidinium Chloride, 2PP2A, 2-amino-4-(methylthio)butanoic acid, ATGRP7, acinusS, ATGRP8, Trans Acting siRNA, NEC, dSET, dSet, Trecator, PTBR, Chronic, peptidos, ETH, metionina, 4-(2-hydroxyethyl)-, tasiRNA, PTHB1, ETP, proto-oncogene c-Kit, RNA, Trans-Acting, Guanidine Monohydrate, Guanidine Nitrate, chronic obstructive airways disease NOS, COAD, Proteins, shRNA, Methyl alcohol, chloridohydrogen, backward, cosuppression, COLD - Chronic obstructive lung disease, L-Isomer, Cell, chronic, mKIAA0670, Engine, Small Hairpin RNA, Short Interfering, polypeptide, Interference, Temperatures, I-2PP2A, KIT ligand receptor activity, C18, Acetate, chemical analysis, Long Term Effects, Dm I-2, Nitrate, 5alpha, MFS1, Sodium, MIXL, MeOH, (COPD), chronic airway obstruction, soda lye, eagle-Barrett syndrome, chronic obstructive, L-Lysine, Silencing, CAL - Chronic airflow limitation, Met, XKrk1, Post-Transcriptional Gene Silencings, Guanidine Monohydrobromide, AU020952, Small Interfering RNA, Guanidine, Col4a-1, Guanidine Sulfate, ensemble, etionamida, Posttranscriptional, prophylaxis, Separations, GR-RBP7, Striated muscle activator of Rho-dependent signaling, GR-RBP8, Chloride, hydrogen phosphorus, lipofectamine 2000, CD117, mDRC, Longterm Effects, ME-IV, plan specification, Gene Proteins, Post-Transcriptional, hydrogen phosphide, C-Kit, siRNA, control, Ssm, chronic obstructive lung disease (disorder), xkl-1, Aetznatron, liquid chromatography tandem mass spectrometry, Post-Transcriptional Gene Silencing, Sulfate, Enisyl, hydrochloric acid, Methoxide, reversed, Repeat-Associated siRNA, chronic obstructive pulmonary disease, liquid chromatography tandem mass spectroscopy, LF 2000, IPP2A2, Bru, T22F8.160, determination, and rna binding 2, RADIATION SENSITIVE23B, Chronic Airflow Obstructions, Small Hairpin, classic hairy cell leukaemia, Monohydrate, Guanidine Sulfate (2:1), HEPES Monosodium Salt, Hydrogenchlorid, Xkl-1, peptide, Techniques, L-Isomer Methionine, Gsfsco1, Methionine, Trans Acting, peptido, BANF, chronic obstructive airways disease NOS (disorder), Min, Chronic Obstructive Pulmonary Disease (COPD), prevention and control, Gsfsco5, Injectables, Effect, DmelCG42273, MIX, wood alcohol, SOW3, Svc, HEPES Monosodium, 3-hydroxy-5-estrane-17-carbonitrile, COLD (chronic obstructive lung disease), LCMSMS, Man (Taxonomy), reference sample, peptides, NEC in ICD9CM_2006, TAF-I, 2610036I19Rik, 2610510L13Rik, min, epsilon-diaminocaproic acid, Ethioniamide, mAPC, IBP, Phosphate, purification, quelling, INSDC_feature:ncRNA, Chronic airflow limitation, preventive measures, IGAAD, fSAP152, Methodological Studies, 1-Piperazineethanesulfonic acid, DmelCG10574, GLYCINE RICH PROTEIN 7, ppm, Guanidine Sulfate (1:1), TEAB, Sodium Methoxide, Bladder pain syndrome, Reagents, glycine-rich RNA-binding protein 8, Natriumhydroxid, hydroxyde de sodium, Sl, GPHYSD2, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, Racemethionine, Long-Term Effects, Transfections, CHRONIC, phapii, Interfering RNA, obstructive lung disease, Trans-Acting siRNA, Monohydrochloride, Alcohol, Modern, LC-MS/MS, 2-Amino-4-(methylthio)butyric acid, Dmel_CG7826, Ethyonomide, StF-IT-1, Tr-kit, Th, mHR23B, Search, classic hairy cell leukemia, Airflow Obstructions, pulmonary disease (COPD), S-adenosyl-L-methionine:thiol S-methyltransferase activity, transfect, Ionen, Small Scan, CHRONIC OBSTRUCTIVE, chronic obstructive pulmonary disease and allied conditions, lysine, Chronic airway disease, kl1-A, Henson's node, NOS, KIT, Short Interfering RNA, RNA Silencing, Hairpin RNA, Scan, Carbinol, PlexA1, fixed, Dmel_CG7835, COPD NOS, carbinol, CHRONIC OBSTRUCTIVE LUNG DIS, Mnb, MNB, parent ion, tyrosine-protein kinase Kit, Chronic airway obstruction, MILD1, absence of, Painful Bladder Syndrome, NaOH, cold, PlexB, PlexA, MS/MS, Xylella fastidiosa str. Temecula1, Sonications, HCl, Guanidine Monohydrochloride, L-Cysteine, kit, MASS, CG4299, AW124434, Plex1, Methodological Study, Trichloromethane, chloracetamide, Chronic Airflow Obstruction, nanospray, Wood, precursor ion, COPD - Chronic obstructive pulmonary disease, chronic obstructive airways disease, Biocatalyst, P58, Polypeptide, obstructive pulmonary disease (COPD), HEPES, Co-Suppression, Etionamide, PLEXB, i2pp2a, COLD, chronic obstructive lung disease, Bladder Pain Syndrome, human being, Cysteine Hydrochloride, Procedures, DISEASE (COPD), Reagent, p58, SCF receptor activity, L Isomer, FBN, Gene, Methyl, CG11081, circadian rhythm, ACINUS, Methylalkohol, PHAPII, LC-MS-MS, Cold, method, Short Hairpin RNA, Pulmonary Disease, scfr, Homo sapiens, Ms1, ECTOL1, Injection, Scan RNA, method used in an experiment, Studies, L-Methionine, Wood Alcohol, D-Plex A, Del(8)44H, F20B17_8, SCFR, Separated, cloruro de hidrogeno, Reagents and Indicators, Pedameth, Pro-Mega, Guanidium Chloride, Search Engines, Cold Temperatures, Fdc, MS1, MS2, iones, Etioniamid, ipp2a2, phosphane, soude caustique, Chronic Obstructive, Indicators, Xylella fastidiosa (strain Temecula1 / ATCC 700964), OCTD, 10^[-6], wood naphtha, taf-ibeta, stem node, male sterility 1, LF-2000, N-2-Hydroxyethylpiperazine-N'-2'-ethanesulfonic Acid, Long-Term Effect, HHR23B, Guanidine Hydrochloride, thiol methyltransferase activity, Controlled, COPD, Controlling, COAD - Chronic obstructive airways disease, DYRK1, DBI, DL-Methionine, not elsewhere classified, posttranscriptional gene silencing by siRNA, igaad, plex, PULM DIS CHRONIC OBSTRUCTIVE, Guanidinium, Peptide, Chronic obstructive pulmonary disease finding (finding), group, 2-ethyl-4-thiopyridylamide, RNAi, [HCl], LC/MS/MS, PKBS, WI-38, Protein, caustic soda, I2PP2A, Hydrochloride, Guanidine Sulfite (1:1), Dyrk1, GLYCINE-RICH RNA-BINDING PROTEIN 7, (3alpha, tandem MS, WMS2, Data Base, chronic obstructive airway disease, DDA, Temperature, Separation, c-KIT, with urinary tract Abnormality and cryptorchidism, PRSS, nodal stem, MALE STERILITY 1 PROTEIN, Posttranscriptional Gene Silencing, Dops, CC1, Tripcellim, N 2 Hydroxyethylpiperazine N' 2' ethanesulfonic Acid, sample population, Protein Gene Products, Trypure, dSET/TAF-Ibeta, c-kit, 2610030F17Rik, Ion, 2-carboxyethyl, wood spirit, Modern Man, SSKS, alpha-amino-gamma-methylmercaptobutyric acid, cold (chronic obstructive lung disease), Peptid, Chronic Obstructive Lung Disease, assay, SCH, AA407739, 6-diaminohexanoic acid, 3-OHECN"],"additional_accession":[]},"is_claimable":false,"name":"TMTpro 16-plex analysis of siRAD23B and siControl in replicatively and ETP-treated senescent cells","description":"Replicatively-senescent and ETP-treated senescent WI-38 cells were transfected with siRNAs (Stealth Select RNAi RAD23B siRNA #1 and siGENOME non-targeting control siRNA #2) using Lipofectamine RNAiMAX in four biological replicates. At 72 h after transfection, the cells were washed twice with cold-PBS and lysed in 6 M guanidine-HCl containing 100 mM HEPES-NaOH (pH7.5), 10 mM Tris (2-carboxyethyl) phosphine, and 40 mM chloroacetamide. The lysates were dissolved by heating and sonication and then centrifuged at 20,000 g for 15 min at 4°C. The supernatants were recovered, and proteins (40 µg each) were purified by methanol-chloroform precipitation and solubilized by 0.1% RapiGest SF (Waters) in 50 mM triethylammonium bicarbonate. The proteins were digested with 0.5 µg trypsin/Lys-C mix (Promega) at 37°C overnight. Peptides (12.5 µg) from each sample were labeled with 0.25 mg of TMTpro 16-plex reagents (Thermo Fisher Scientific) and combined and fractionated using the Pierce high pH reversed-phase peptide fractionation kit. Nine fractions were collected using 5%, 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, and 50% ACN. LC-MS/MS analysis of the resultant peptides (1 µg) from each fraction except the first was performed on an EASY-nLC 1200 UHPLC connected to a Q Exactive Plus mass spectrometer through a nanoelectrospray ion source (Thermo Fisher Scientific). The peptides were separated on a 75-μm-inner-diameter, 150-mm C18 reversed-phase column (Nikkyo Technos) with a linear gradient of 4–24% for 0–140 min and 24–36% for 140–180 min, followed by an increase to 80% ACN for 10 min. The mass spectrometer was operated in data-dependent acquisition mode with a top 15 MS/MS method. MS1 spectra were measured with a resolution of 70,000, an AGC target of 3e6, and a mass range from 375 to 1,400 m/z. MS/MS spectra were triggered at a resolution of 35,000, an AGC target of 1e5, an isolation window of 0.4 m/z, a maximum injection time of 100 ms, and a normalized collision energy of 31. Dynamic exclusion was set to 20 s. Raw data were directly analyzed against the SwissProt database restricted to Homo sapiens using Proteome Discoverer (v.2.4) with Sequest HT search engine for identification and TMT quantification. The search parameters were the following: (a) trypsin as an enzyme with up to two missed cleavages; (b) precursor mass tolerance of 10 ppm; (c) fragment mass tolerance of 0.02 Da; (d) TMTpro of lysine and peptide N-terminus and carbamidomethylation of cysteine as fixed modifications; and (e) oxidation of methionine as a variable modification. Peptides were filtered at a false discovery rate <0.01 using the Percolator node. TMT quantification was performed using the Reporter Ions Quantifier node.","dates":{"publication":"Sat Jul 22 00:00:00 BST 2023"},"accession":"PXD028626","cross_references":{"TAXONOMY":["9606"],"pubmed":["37541257"]}}