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Young rosettes (leaves 6-10 and the meristem) were harvested. Three plants were pooled together per replicate and 4 replicates were harvested. Protein extraction, quantification, reduction, and alkalization were done as in Zhang et al. (2015). Protein precipitation was done by the methanol/chloroform method as in Zhang, et al. (2018) and sequential trypsin digestion performed at a protease: protein ratio of from 1:100 to final 1:50 (w/w). Peptide concentration was determined using a Pierce Quantitative Colorimetric Peptide Assay kit (23,275, Thermo Scientific). Labelling was performed by mixing 100 µL of peptide (1 µg/µL) with 40 µL (~0.25mg) TMTpro™ stock in acetonitrile (TMTpro™ 16plex Mass Tag Isobaric Labelling Reagent Set Thermo Fisher Scientific) and then incubated for 1 h at room temperature.    This was followed by quenching with 8 µL of 5% hydroxylamine solution and incubation at room temperature for 15 min. Equal amounts of each prepared peptide were combined in a new tube. The solvent composition was adjusted to acetonitrile <5 % and 1 % trifluoracetic acid (HPLC grade 99.5% 044630.AE Alfa Aesar) for desalting with Sep-Pak® vac tC18 cartridge [100 mg] (Waters).  High-pH first dimension reverse-phase fractionation. The following LC conditions were used for the fractionation of the TMT samples: desalted peptides were resuspended in 0.1 mL 20 mM ammonium formate (pH 10.0) + 4 % (v/v) acetonitrile. Peptides were loaded onto an Acquity bridged ethyl hybrid C18 UPLC column (Waters; 2.1 mm i.d. x 150 mm, 1.7 µm particle size), and profiled with a linear gradient of 5-60% acetonitrile + 20 mM ammonium formate (pH 10.0) over 60 min, at a flow-rate of 0.25 mL/min. Chromatographic performance was monitored by sampling eluate with a diode array detector (Acquity UPLC, Waters) scanning between wavelengths of 200 and 400 nm. Samples were collected in 1 min increments and reduced to dryness by vacuum centrifugation.  LC-MS/MS Dried fractions from the high pH reverse-phase separations were resuspended in 0.1% formic acid and placed into a glass vial. 1 μL of each fraction was injected by the HPLC autosampler and separated by the LC method detailed below. Fractions were combined into pairs  and were analysed by LC-MS/MS. LC-MS/MS experiments were performed using a Dionex Ultimate 3000 RSLC nanoUPLC (Thermo Fisher Scientific Inc, Waltham, MA, USA) system and a Orbitrap Lumos™ Tribrid™ mass spectrometer (Thermo Fisher Scientific Inc, Waltham, MA, USA). Peptides were loaded onto a pre-column (Thermo Scientific PepMap 100 C18, 5 mm particle size, 100 Å pore size, 300 mm i.d. x 5 mm length) from the Ultimate 3000 auto-sampler with 0.1 % formic acid for 3 min at a flow rate of 10 μL/min. After this period, the column valve was switched to allow elution of peptides from the pre-column onto the analytical column. Separation of peptides was performed by C18 reverse-phase chromatography at a flow rate of 300 nL/min using a Thermo Scientific reverse-phase nano Easy-spray column (Thermo Scientific PepMap C18, 2mm particle size, 100 Å pore size, 75 mm i.d. x 50 cm length). Solvent A was water + 0.1 % formic acid and solvent B was 80 % acetonitrile, 20 % water + 0.1 % formic acid. The linear gradient employed was 2-40 % B in 93 min.  (Total LC run time was 120 min, including a high organic wash step and column re-equilibration). The eluted peptides from the C18 column LC eluant were sprayed into the mass spectrometer by means of an Easy-Spray source (Thermo Fisher Scientific Inc.). All m/z values of eluting peptide ions were measured in an Orbitrap mass analyzer, set at a resolution of 120,000 and were scanned between m/z 380-1500 Da. Data dependent MS/MS scans (Top Speed) were employed to automatically isolate and fragment precursor ions by collision-induced dissociation [CID, Normalised Collision Energy (NCE): 35 %] which were analysed in the linear ion trap. Singly charged ions and ions with unassigned charge states were excluded from being selected for MS/MS and a dynamic exclusion window of 70 s was employed. The top 10 most abundant fragment ions from each MS/MS event were then selected for a further stage of fragmentation by Synchronous Precursor Selection (SPS) MS3 (1) in the HCD high energy collision cell using HCD [High energy Collisional Dissociation, (NCE: 55 %)]. The m/z values and relative abundances of each reporter ion and all fragments (mass range from 100-500 Da) in each MS3 step were measured in the Orbitrap analyser, which was set at a resolution of 50,000.  This was performed in cycles of 10 MS3 events before the Lumos instrument reverted to scanning the m/z ratios of the intact peptide ions and the cycle continued.The sample process was done by Hongtao Zhang from Rothamsted. RP was performed by Renata Feret amd Mass spec run was done by Mike Deery."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["Raw data were searched against the Arabidopsis TAIR10; cRAP (version of the data) database using MASCOT version 2.7.0 (Matrix Science, London, UK) and PROTEOME DISCOVERERTM v. 2.5.0.400 as described previously employing Top 10 peaks filter node and percolator nodes and reporter ions quantifier with Trypsin enzyme specificity with a maximum of one missed cleavage. Carbamidomethylation (+57.021 Da) of cysteine and TMTpro™ isobaric labelling (+304.207) of lysine and N-termini were set as static modifications while methionine oxidation (+15.996) was considered dynamic. Mass tolerances were set to 10 ppm for MS and 0.8 Da for MS/MS. For quantification, TMTpro method was used, and integration tolerance was set to Xmmu, Integration Method was set as centroid sum. Purity correction factor was set according the TMTpro™ product sheet. Each reporting ion was divided by the sum of total ions and normalized by medians of each sample. Log transformation ensured a homogeneity and normal distribution of the variances. Only proteins represented by two or more peptides were considered for further analysis. Heatmaps were generated by applying a z-score transformation using normalized log2 transformed abundance before performing the hierarchical clustering. Differential expression of proteins was determined using limma (Ritchie et al., 2015). Proteins were designated as differentially expressed when their FDR-adjusted p-value was below 0.05 and their absolute log2 fold change was above 1.PD search was performed by Yagnesh Umrania in Cambrdige center for proteomics."],"omics_type":["Proteomics"],"labhead":["Hongtao Zhang"],"instrument_platform":[""],"labhead_affiliation":["Rothamsted Research, Harpenden, AL5 2JQ, UK"],"species":["Arabidopsis Thaliana (mouse-ear Cress)"],"submission_type":["PARTIAL"],"publication":["42191641 Rankenberg T, Sanclemente MA, Zhang H, Leeggangers HA, Orozco-Granados O, Devaiah MB, Chao JR, van Veen H, Theodoulou FL, Sasidharan R. Distinct processes contributing to post-submergence recovery determine leaf age-specific flood resilience in Arabidopsis. Plant Physiol. 2026:kiag317 10.1093/plphys/kiag317"],"submitter_mail":["hongtao.zhang@rothamsted.ac.uk"],"submitter_affiliation":["Rothamsted Research, Harpenden, AL5 2JQ, UK"],"submitter_country":["United Kingdom"],"pubmed_abstract":["While the molecular mechanisms mediating submergence tolerance have been extensively studied, those underpinning age-dependent resilience remain poorly characterized. In Arabidopsis thaliana, submergence elicits a leaf age-dependent phenotype in which senescence and death progress across an age gradient starting with older leaves. Here, we sought to investigate the mechanisms mediating the observed differential flood resilience by interrogating leaf age-specific transcriptome and proteome changes during submergence and recovery. Following submergence, most age-dependent differences were in the magnitude or speed of transcript abundance changes, whereas qualitative leaf age-dependent responses were most apparent during recovery. This included a strong desiccation response in old leaves despite a stronger abscisic acid (ABA)-signaling response. Physiological measurements suggested that faster dehydration was facilitated by submergence-mediated reduction of ABA sensitivity but was not associated with differences in stomatal conductance or cuticle integrity. We also observed a stronger induction in young shoot tissue of genes associated with endoplasmic reticulum stress and the unfolded protein response. Mutants disabled in both unfolded protein response signaling branches were affected in new leaf formation and in the ability to restore the proteome, but not in senescence, suggesting that young tissues activate endoplasmic reticulum stress recovery to permit continuation of growth. Among mitochondrial membrane proteins differentially regulated in young leaves, loss of mitochondrial voltage-dependent anion channel function impacted submergence-recovery tolerance. Our data reveal multiple mechanisms underlying leaf age-dependent differential submergence recovery and demonstrate how an interplay between age-related developmental traits and stress signaling pathways determines tolerance."],"pubmed_title":["Distinct processes contributing to post-submergence recovery determine leaf age-specific flood resilience in Arabidopsis."],"pubmed_authors":["Rankenberg Tom T, Sanclemente Maria Angelica MA, Zhang Hongtao H, Leeggangers Hendrika A C F HACF, Orozco-Granados Omar O, Devaiah Muthanna Biddanda MB, Chao Janet Rong JR, van Veen Hans H, Theodoulou Frederica L FL, Sasidharan Rashmi R"],"additional_accession":[]},"is_claimable":false,"name":"Leaf-age specific flood resilience in Arabidopsis thaliana is determined by distinct processes contributing to post-submergence recovery","description":"While the molecular mechanisms mediating submergence tolerance have been extensively studied, those underpinning age-dependent resilience remain poorly characterized. In Arabidopsis thaliana, submergence elicits a leaf-age dependent phenotype in which senescence and death progress across an age gradient starting with older leaves. Here we sought to investigate the mechanisms mediating this observed differential flood resilience by interrogating leaf age-specific transcriptome and proteome changes during submergence and recovery. Following submergence, most age-dependent differences were in the magnitude or speed of transcript abundance changes, whereas qualitative leaf-age dependent responses were most apparent during recovery. This included a strong desiccation response in old leaves despite a stronger ABA-signaling response. Physiological measurements suggested that faster dehydration was mediated by a combination of submergence-mediated reduction of ABA sensitivity and higher conductance in old leaves. We also observed a stronger induction in young shoot tissue of genes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). Mutants disabled in the two UPR signaling branches were affected in new leaf formation and the ability to restore the proteome, but not in senescence, suggesting that young tissues activate ER stress recovery to permit continuation of growth. Of the mitochondrial membrane proteins differentially regulated in young leaves, loss of mitochondrial voltage-dependent anion channel function impacted submergence-recovery tolerance. Our data reveal multiple mechanisms underlying leaf age-dependent differential submergence recovery and demonstrate how tolerance is determined by an interplay between age related developmental traits and stress signaling pathways.","dates":{"publication":"2026-08-14","submission":"2025-08-07"},"accession":"PXD067068","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:475174","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:460523","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:2925","NEWT:214053","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:29829","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:90690","NEWT:1436183","NEWT:300273","NEWT:4232","NEWT:416348","NEWT:11298","NEWT:4236","NEWT:7742","NEWT:196627","NEWT:200308","NEWT:242507","NEWT:200302","NEWT:870435","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:2666255","NEWT:999810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