Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_18.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_16.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_17.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_15.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/240529_RU_YuLi_B_01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065691/txt.zipprimaryOK200Nakagami@mpipz.mpg.deSara Christina StolzeData-dependent acquisitionAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryPlant-environment interactionsSignal transductionAp-msUv-b photoreceptorMarchantiaUv-bProtein-protein interactionsPhotomorphogenesisUvr8Acclimationhttps://www.ebi.ac.uk/pride/archive/projects/PXD065691Plant CellAP–MS was performed using a Marchantia transgenic line expressing ProMpUVR8:GFP-MpUVR8, with wild-type Tak-1 and a ProMpUBQ2:mVenus line as negative controls. Plants were grown for 7 days under continuous white light (50 μmol m⁻² s⁻¹) without UV-B, or under continuous white light (50 μmol m⁻² s⁻¹) supplemented with narrowband UV-B (1.5 μmol m⁻² s⁻¹) followed by a 20 min broadband UV-B exposure (25 μmol m⁻² s⁻¹) immediately prior to harvest. Total protein was extracted and GFP-Trap agarose beads (Chromotek) were used for affinity purifications. Eluted proteins were subjected to LC-MS/MS analysis. Sample preparation and LC-MS/MS data acquisition: enriched proteins were submitted to an on-bead digestion using trypsin. In brief, dry beads were re-dissolved in 25 µL digestion buffer 1 (50 mM Tris, pH 7.5, 2M urea, 1mM DTT, 5 ng/µL trypsin) and incubated for 30 min at 30 °C in a Thermomixer with 400 rpm. Next, beads were pelleted and the supernatant was transferred to a fresh tube. Digestion buffer 2 (50 mM Tris, pH 7.5, 2M urea, 5 mM CAA) was added to the beads, after mixing the beads were pelleted, the supernatant was collected and combined with the previous one. The combined supernatants were then incubated o/n at 32°C in a Thermomixer with 400 rpm; samples were protected from light during incubation. The digestion was stopped by adding 1 µL TFA and desalted with C18 Empore disk membranes according to the StageTip protocol (Rappsilber et al., 2003). Dried peptides were re-dissolved in 2% ACN, 0.1% TFA (10 µL) for analysis. Samples were analyzed using an EASY-nLC 1200 (Thermo Fisher) coupled to a Q Exactive Plus mass spectrometer (Thermo Fisher). Peptides were separated on 16 cm frit-less silica emitters (New Objective, 75 µm inner diameter), packed in-house with reversed-phase ReproSil-Pur C18 AQ 1.9 µm resin (Dr. Maisch). Peptides were loaded on the column and eluted for 115 min using a segmented linear gradient of 5% to 95% solvent B (0 min : 5%B; 0-5 min -> 5%B; 5-65 min -> 20%B; 65-90 min ->35%B; 90-100 min -> 55%; 100-105 min ->95%, 105-115 min ->95%) (solvent A 0% ACN, 0.1% FA; solvent B 80% ACN, 0.1%FA) at a flow rate of 300 nL/min. Mass spectra were acquired in data-dependent acquisition mode with a TOP15 method. MS spectra were acquired in the Orbitrap analyzer with a mass range of 300–1750 m/z at a resolution of 70,000 FWHM and a target value of 3×106 ions. Precursors were selected with an isolation window of 1.3 m/z (Q Exactive Plus). HCD fragmentation was performed at a normalized collision energy of 25. MS/MS spectra were acquired with a target value of 105 ions at a resolution of 17,500 FWHM, a maximum injection time (max.) of 55 ms and a fixed first mass of m/z 100. Peptides with a charge of +1, greater than 6, or with unassigned charge state were excluded from fragmentation for MS2, dynamic exclusion for 30s prevented repeated selection of precursors.PrideData analysis: raw data were processed using MaxQuant software (version 1.6.3.4, http://www.maxquant.org/) (Cox and Mann, 2008) with label-free quantification (LFQ) and iBAQ enabled (Tyanova et al., 2016). MS/MS spectra were searched by the Andromeda search engine against a combined database containing the sequences from M. polymorpha (MpTak_v6.1r2.protein.fasta; https://marchantia.info/download/MpTak_v6.1r2/) and sequences of 248 common contaminant proteins and decoy sequences. Trypsin specificity was required and a maximum of two missed cleavages allowed. Minimal peptide length was set to seven amino acids. Carbamidomethylation of cysteine residues was set as fixed, oxidation of methionine and protein N-terminal acetylation as variable modifications. The match between runs option was enabled. Peptide-spectrum-matches and proteins were retained if they were below a false discovery rate of 1% in both cases. Statistical analysis of the MaxLFQ values was carried out using Perseus (version 1.5.8.5, http://www.maxquant.org/). Quantified proteins were filtered for reverse hits and hits “identified by site” and MaxLFQ values were log2 transformed. After grouping samples by condition only those proteins were retained for the subsequent analysis that had three valid values in one of the conditions. Missing values were imputed from a normal distribution (1.8 downshift, separately for each column). Volcano plots were generated in Perseus using an FDR of 5% and an S0=1. Significantly different proteins were identified using a p-value cutoff of < 0.01 and a log10 fold change threshold of ±1.0ProteomicsHirofumi NakagamiBasic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, GermanyPARTIALMarchantia Polymorphastolze@mpipz.mpg.de41985038 Liang Y, Podolec R, Chappuis R, Defossez E, Glauser G, Roetzer J, Stolze SC, Dolan L, Nakagami H, Demarsy E, Ulm R. Conservation and divergence of UVR8 photoreceptor-mediated UV-B signaling in Marchantia polymorpha. Plant Physiol. 2026 201(2):kiag218 10.1093/plphys/kiag218Plant Proteomics and Mass Spectrometry Group Max Planck Institute for Plant Breeding Research Carl-von-Linné Weg 10 50829 CologneGermanyUltraviolet-B radiation (UV-B) poses a major challenge to all forms of plant life. The liverwort Marchantia (Marchantia polymorpha) serves as a key model organism for studying signaling pathways and inferring their evolution throughout the green lineage. Marchantia expresses key components of UV-B signaling, including the photoreceptor UV RESISTANCE LOCUS 8 (MpUVR8), the WD40-repeat protein REPRESSOR OF UV-B PHOTOMORPHOGENESIS (MpRUP), the E3 ubiquitin ligase complex CONSTITUTIVELY PHOTOMORPHOGENIC 1/SUPPRESSOR OF phyA-105 (MpCOP1/MpSPA), and the transcriptional regulator ELONGATED HYPOCOTYL 5 (MpHY5). Here, we show that whereas the core UVR8 photocycle is well conserved, regulatory roles of SPA and HY5 diverged during plant evolution. Unlike the case in Arabidopsis (Arabidopsis thaliana) and in contrast to the strong Mpcop1 mutant phenotype, Mpspa mutants developed only a very weak constitutive photomorphogenesis phenotype, indicating that COP1 function is much more independent of SPA in Marchantia than in Arabidopsis. Moreover, in contrast to Arabidopsis SPAs, Mpspa showed enhanced UV-B acclimation and UV stress tolerance, indicating that MpSPA is a negative regulator of MpUVR8 signaling. Similar to Arabidopsis HY5/HYH, MpHY5 functioned antagonistically to MpCOP1, but its role in UV-B-mediated gene expression changes was more limited. Our findings demonstrate that although core components of UV-B signaling existed in the last common ancestor of extant land plants, regulatory interactions have diversified in different lineages since their divergence more than 400 million years ago.Conservation and divergence of UVR8 photoreceptor-mediated UV-B signaling in Marchantia polymorpha.Liang Yuanke Y, Podolec Roman R, Chappuis Richard R, Defossez Emmanuel E, Glauser Gaétan G, Roetzer Johannes J, Stolze Sara Christina SC, Dolan Liam L, Nakagami Hirofumi H, Demarsy Emilie E, Ulm Roman RfalseConservation and divergence of UVR8-COP1/SPA-HY5 signaling in UV-B responses of Marchantia polymorphaUltraviolet-B radiation (UV-B) poses a major challenge to all forms of plant life. The liverwort Marchantia polymorpha (Marchantia) serves as a key model organism to study signaling pathways and to infer their evolution throughout the green lineage. Marchantia expresses key components of UV-B signaling, including the photoreceptor UV RESISTANCE LOCUS 8 (MpUVR8), the WD40-repeat protein REPRESSOR OF UV-B PHOTOMORPHOGENESIS (MpRUP), the E3 ubiquitin ligase complex CONSTITUTIVELY PHOTOMORPHOGENIC 1 / SUPPRESSOR OF phyA-105 (MpCOP1/MpSPA), and the transcriptional regulator ELONGATED HYPOCOTYL 5 (MpHY5). Here, we show that MpUVR8 exists as a homodimer in its ground-state in vivo, then monomerizes and accumulates in the nucleus upon UV-B activation. Activated MpUVR8 interacts with MpCOP1, triggering growth inhibition, gene expression changes, biosynthesis of UV-absorbing metabolites, and photoprotection, which overall contributes to UV-B stress tolerance. MpRUP facilitates redimerization of MpUVR8 and Mprup null mutants show enhanced UV-B photomorphogenesis, indicating that MpRUP efficiently represses MpUVR8 signaling. Unlike the case in Arabidopsis and in contrast to the strong Mpcop1 mutant phenotype, Mpspa mutants develop only a weak constitutive photomorphogenesis phenotype, indicating that COP1 function is more independent of SPA in Marchantia than in Arabidopsis. Interestingly, however, Mpspa is linked with a hyper-responsive UV-B phenotype, suggesting that MpSPA is a negative regulator of MpUVR8 signaling. Our findings demonstrate that core components of UV-B signaling existed in the last common ancestor of extant land plants; however, regulatory interactions have diversified in different lineages since their divergence more than 400 million years ago.2026-06-292025-07-02PXD065691NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:111205NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:641809NEWT:317447NEWT:4688NEWT:111225NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:1912919NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:270643NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2709072NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:294607NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:235443NEWT:108458NEWT:5936NEWT:320637NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:1071661NEWT:470NEWT:5911NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:9031NEWT:27292NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:8655NEWT:5147NEWT:28104NEWT:407821NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:40674NEWT:1194669NEWT:51329NEWT:443906NEWT:519NEWT:2510939NEWT:6063NEWT:1328388NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:4232NEWT:416348NEWT:11298NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:430615NEWT:563041NEWT:72664NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:8644NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:192222NEWT:9963NEWT:1617910NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NCBITaxon:12637NEWT:38727NEWT:8618NEWT:70448NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:10136NEWT:38942NEWT:4762NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:869728NEWT:6938NCBITaxon:39054NEWT:1736309NEWT:4751NEWT:194963NEWT:15819NEWT:109461NEWT:1085956NEWT:6928NEWT:1239NEWT:36745NEWT:400727NEWT:272563NEWT:11009NEWT:3885NEWT:3888NEWT:649408NEWT:6915NEWT:101510NEWT:3880NEWT:272559NEWT:216816NEWT:153151NEWT:515849NEWT:10141NEWT:95767NEWT:466585NEWT:1000589NEWT:85963NEWT:29NEWT:85962NEWT:42197NEWT:143361NEWT:1299NEWT:424718NEWT:316407NEWT:1794699NCBITaxon:183674NEWT:167387NEWT:84645NEWT:1123294NEWT:209285NEWT:211586NEWT:747078NEWT:1282NEWT:1283NEWT:1000561NEWT:2133NEWT:294381NEWT:197NEWT:1390363NEWT:35889NEWT:406072NEWT:1454958N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