Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/Histone_Search.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_MR-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_72h_SM-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_SM-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_SM-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_72h_Ctrl-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_MR-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_Ctrl-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_72h_Ctrl-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_72h_MR-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_72h_SM-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_MR-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_72h_MR-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_SM-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_72h_SM-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_Ctrl-1-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_72h_Ctrl-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_Ctrl-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_Ctrl-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_5h_MR-2-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/20220219_Simone_Kaylah_72h_MR-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069602/Histones_Human_SwissProt_Sept2020.fastaprimaryOK200simone.sidoli@einsteinmed.eduSimone SidoliMass SpectrometryBottom-up proteomicsNot availablePhosphorylationLongevityMethylationAutophagyLifespanMethionine restrictionhttps://www.ebi.ac.uk/pride/archive/projects/PXD069602Histones were isolated from a protocol adapted from Fukuma, et. al32. Yeast were cultured in 1L of SC media and the equivalent of 400 OD600nm of cells were collected (i.e., 800 ml of culture at 0.5 OD600nm) by centrifugation at 4,691 x g for 5 min. The pellet was washed once with ice cold water and then washed with 20-50 ml ice cold SP buffer (20 mM HEPES 7.4, 1.2 M sorbitol, 10 mM DTT). The pellet was resuspended in 10 ml SP buffer + 5 mg/ml yeast lytic enzyme and incubated at 30 ºC for 20-30 minutes. When spheroplasting was complete, the sample was spun in a tabletop centrifuge at 4,000 rpm for 5 minutes at 4 ºC and washed with 10 ml SP buffer. Next, the pellet was resuspended in 10 ml Buffer L (20 mM HEPES 7.4, 18% Ficoll 400, 20 mM KCl, 5mM MgCl2, 0.5 mM spermidine, 1 mM EDTA, protease inhibitors, 3 mM DTT, 1 mM PMSF) and transferred to a 40 ml dounce homogenizer with type B pestle. After completing 20 strokes, sample was transferred to a conical tube and diluted with 40 ml Buffer S (Buffer L with 2.4 M sorbitol instead of Ficoll). Sample was then spun at 4000 x g for 5 minutes; then the supernatant was removed and spun at 14,400 x g for 20 minutes. The pellet was resuspended in 10 ml Buffer NIB (15 mM MES 6.6, 0.25 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.8% TritonX-100, 1 mM PMSF, 1 mM DTT). After a 20 minute incubation on ice, the sample was pelleted at 14,400 x g for 20 minutes. Two 5-minute wash cycles at 5,050 x g in Buffer A (10 mM Tris 8, 75 mM NaCl, 0.5% NP-40, 1 mM PMSF) were completed, and then the pellet was resuspended in 9 ml Buffer B (Buffer A with 400 mM NaCl, no NP-40). 1 ml of 4 N H2SO4 was added dropwise, vortexing after each drop, to 0.4 N final. Sample was then nutated at 4 ºC for 1 hour. After nutating, sample was spun down at 14,400 x g for 20 minutes and the supernatant was transferred to a new tube. Then, the pellet was re-extracted with 1 ml 4 N H2SO4 in 9 ml Buffer B without prolonged incubation and spun down. The supernatants were combined, and 100% TCA was added to 20% final concentration. After a final 30-minute ice incubation, the sample was spun down at 14,400 x g for 20 minutes, washed with acetone + 0.1% HCl for 20 minutes, and then washed with acetone for another 20 minutes. Pellet was left to air dry and then resuspended in 100-200 µl of 50 mM ammonium bicarbonate. The mass spectrometry was performed as described previously . Briefly, histones were subjected to derivatization using 5 µL of propionic anhydride and 14 µL of ammonium hydroxide (all Sigma Aldrich) to balance the pH at 8.0. The mixture was incubated for 15 min and the procedure was repeated. Histones were then digested with 1 µg of sequencing grade trypsin (Promega) diluted in 50mM ammonium bicarbonate (1:20, enzyme:sample) overnight at room temperature. Derivatization reaction was repeated to derivatize peptide N-termini. The samples were dried in a vacuum centrifuge. Sample desalting – Prior to mass spectrometry analysis, samples were desalted using a 96-well plate filter (Orochem) packed with 1 mg of Oasis HLB C-18 resin (Waters). Briefly, the samples were resuspended in 100 µl of 0.1% TFA and loaded onto the HLB resin, which was previously equilibrated using 100 µl of the same buffer. After washing with 100 µl of 0.1% TFA, the samples were eluted with a buffer containing 70 µl of 60% acetonitrile and 0.1% TFA and then dried in a vacuum centrifuge. LC-MS/MS Acquisition and Analysis – Samples were resuspended in 10 µl of 0.1% TFA and loaded onto a Dionex RSLC Ultimate 300 (Thermo Scientific), coupled online with an Orbitrap Fusion Lumos (Thermo Scientific). Chromatographic separation was performed with a two-column system, consisting of a C-18 trap cartridge (300 µm ID, 5 mm length) and a picofrit analytical column (75 µm ID, 25 cm length) packed in-house with reversed-phase Repro-Sil Pur C18-AQ 3 µm resin. Peptides were separated using a 30 min gradient from 1-30% buffer B (buffer A: 0.1% formic acid, buffer B: 80% acetonitrile + 0.1% formic acid) at a flow rate of 300 nl/min. The mass spectrometer was set to acquire spectra in a data-independent acquisition (DIA) mode. Briefly, the full MS scan was set to 300-1100 m/z in the orbitrap with a resolution of 120,000 (at 200 m/z) and an AGC target of 5x10e5. MS/MS was performed in the orbitrap with sequential isolation windows of 50 m/z with an AGC target of 2x10e5 and an HCD collision energy of 30.PrideNot availableHistone peptides raw files were imported into the EpiProfile 2.0 software . From the extracted ion chromatogram, the area under the curve was obtained and used to estimate the abundance of each peptide. In order to achieve the relative abundance of post-translational modifications (PTMs), the sum of all different modified forms of a histone peptide was considered as 100% and the area of the particular peptide was divided by the total area for that histone peptide in all of its modified forms. The relative ratio of two isobaric forms was estimated by averaging the ratio for each fragment ion with different mass between the two species. The resulting peptide lists generated by EpiProfile were exported to Microsoft Excel and further processed for a detailed analysis.ProteomicsSimone SidoliPARTIALDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United StatesSaccharomyces Cerevisiae (baker's Yeast)42160763 Birmingham K, Arslanovic N, Grauer T, Gutierrez I, Chakraborty U, Sidoli S, Tyler J. Methionine Restriction Extends Yeast Lifespan by Activating Non-Nitrogen-Starvation-Induced Autophagy Through Limiting Methylation of Protein Phosphatase 2A. Aging Cell. 2026 25(6):e70550 10.1111/acel.70550simone.sidoli@gmail.comAlbert Einstein College of MedicineUnited StatesMethionine restriction (MR) extends the lifespan and healthspan of numerous eukaryotic organisms, but the molecular mechanisms at play are unclear. Here we find that the ability of MR to extend the budding yeast chronological and replicative lifespans is the consequence of reduced methionine conversion to the methyl donor S-adenosylmethionine (SAM). Mechanistically, the key antiaging event downregulated by MR is the methylation of protein phosphatase 2A (PP2A). In chronological aging cells under MR, unmethylated PP2A no longer dephosphorylates Npr2, a component of the SEACIT complex, resulting in activation of non-nitrogen-starvation (NNS)-induced autophagy. Deletion of genes encoding components of SEACIT or ATG1 (encoding a central player in the initiation of autophagy) blocked the ability of MR to extend lifespan, showing the critical role of the NNS-induced autophagy pathway in lifespan extension by MR. We identify the relevant Npr2 site dephosphorylated by PP2A as serine 362 and show that Npr2 phosphomimetic mutants are sufficient to extend chronological and replicative lifespan. Finally, we discover that MR only during the early stages of chronological aging is sufficient to prolong autophagy and extend lifespan. In addition to elucidating the molecular mechanism of MR-mediated lifespan extension, this study highlights potential therapeutic targets to achieve lifespan and healthspan extension in humans without the challenging long-term dietary changes required to achieve MR.Methionine Restriction Extends Yeast Lifespan by Activating Non-Nitrogen-Starvation-Induced Autophagy Through Limiting Methylation of Protein Phosphatase 2A.Birmingham Kaylah K, Arslanovic Nina N, Grauer Thea T, Gutierrez Ignacio I, Chakraborty Ujani U, Sidoli Simone S, Tyler Jessica JfalseMethionine restriction extends yeast lifespan by activating non-nitrogen-starvation-induced autophagy through limiting methylation of protein phosphatase 2AMethionine restriction (MR) extends the lifespan and healthspan of numerous eukaryotic organisms, but the molecular mechanisms at play are unclear. Here we find that the ability of MR to extend the budding yeast chronological and replicative lifespans is the consequence of reduced methionine conversion to the methyl donor S-adenosyl methionine (SAM). Mechanistically, the key antiaging methylation event downregulated by MR is a methylation of protein phosphatase 2A (PP2A). In chronological aging cells during MR the Npr2 component of the SEACIT complex is no longer able to be dephosphorylated by unmethylated PP2A, resulting in inhibition of Tor1 and activation of non-nitrogen-starvation (NNS)-induced autophagy. Deletion of genes encoding components of SEACIT or ATG1 (encoding a central player in the initiation of autophagy) blocked the ability of MR to extend lifespan, showing the critical role of the NNS-induced autophagy pathway in lifespan extension by MR. We identify the relevant Npr2 site dephosphorylated by PP2A as serine 362 and show that Npr2 phosphomimetic mutants are sufficient to extend chronological and replicative lifespan. Finally, we discover that MR only during the early stages of chronological aging is sufficient to prolong autophagy and extend lifespan. In addition to elucidating the molecular mechanism of MR-mediated lifespan extension, this study highlights potential therapeutic targets to achieve lifespan and healthspan extension in humans without the challenging long-term dietary changes required to achieve MR.2026-06-152025-10-17PXD069602NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:6819NEWT:475174NEWT:111205NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:3765NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:656064NEWT:36630NEWT:383379NEWT:418106NCBITaxon:12721NEWT:10029NEWT:913645NEWT:641809NEWT:1392488NEWT:38815NEWT:317447NEWT:4688NEWT:111225NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:410658NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:156587NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:3714NEWT:270643NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:28174NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:3704NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:8165NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1348799NEWT:33995NEWT:55784NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:1185650NEWT:216778NEWT:294607NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:317047NEWT:491NEWT:460523NEWT:235443NEWT:1757312NEWT:85694NEWT:108458NEWT:5936NEWT:320637NEWT:1078283NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:1640278NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:470NEWT:5911NEWT:748693NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:166313NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:906914NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:381666NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:771870NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:10832NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:9983NEWT:8655NEWT:5147NEWT:28108NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:298176NEWT:227377NEWT:1774284NEWT:40674NEWT:1194669NEWT:51329NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:105487NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:475932NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:28550NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:99488NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:29829NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:441772NEWT:48106NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:300273NEWT:4232NEWT:416348NEWT:11298NEWT:4236NEWT:7742NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:2144189NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:563041NEWT:72664NEWT:36599NEWT:41949NEWT:249161NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:29835NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1801631NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:35231NEWT:8644NEWT:1125630NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:285272NEWT:192222NEWT:9963NEWT:1617910NEWT:637379NEWT:12107NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:186801NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NEWT:194439NCBITaxon:12637NEWT:38727NEWT:218496NEWT:8618NEWT:70448NEWT:300251NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2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