Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/Filename_information.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R08_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20220801_CO_1101RoLo_R01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R13_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R08.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20220801_CO_1101RoLo_R02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R15_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R14_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R12_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20220801_CO_1101RoLo_R03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20220801_CO_1101RoLo_R04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20250317_LC9_CO_1113RoLo_R04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/20221012_CO_1101RoLo_R07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/Exp1_LFQ_R04R15.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/Exp3_TurboID_R05R14.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD065938/Exp2_TurboID_R01R04.zipprimaryOK200rosa.lozano-duran@uni-tuebingen.deIrina Droste-BorelData-dependent acquisitionMass SpectrometryNicotiana benthamianaCajal bodyFluorescence-activated particle sorting (faps)Lc-ms/msProximity labelinghttps://www.ebi.ac.uk/pride/archive/projects/PXD065938Plant CellLeafFAPS Cajal body isolation: Leaf tissues of Nicotiana benthamiana was treated with formaldehyde to stabilize interaction, followed by tissue rupture and then nuclei isolation via fluorescence-activated nuclei sorting. Nuclei were then sonicated to release Cajal bodies, which were subsequently isolated by fluorescence-activated particle sorting and enriched by ultracentrifugation. TurboID-based proximity labeling was performed in Nicotiana benthamiana leaves. Labeling was initiated by supplement leaves with biotin. Leaf tissue discs were homogenized and biotinylated proteins in the supernatant were enriched by streptavidin-coated beads. Samples were in gel digested and extracted peptides were desalted using C18 StageTips. For LFQ analysis, equal peptide amounts were subjected to LC-MS analysis on a VanquishNeo nano-UHPLC coupled to Exploris 480 mass spectrometer via nanoelectrospray ion source (Thermo Fisher Scientific). Peptides were separated using a 49 min segmented gradient of 4-55% HPLC solvent B (80% acetonitrile in 0.1% formic acid. The 20 most intense precursor ions were picked for HCD fragmentation in each scan cycle. TurboID samples were measured with a 49 min segmented gradient of 10–33-50-90% HPLC solvent B at 200 nl/min. Top-seven precursors were fragmentedPrideNot available: Acquired MS data were further analysed using MaxQuant software version 2.2.0.0 (Cox and Mann, 2008) and version 1.6.7.0 for TurboID samples. Spectra were searched against a Nicotiana benthamiana database. Sequences for NbCoilinA and GFP (or TurboID biotin ligase in the case of the pull down samples) were included in the search as additional database. Default search parameters were applied, iBAQ values and in case of LFQ samples also LFQ settings were enabled and match between runs selected for samples within the same group. Statistical analysis was done using Perseus software (version 1.6.15.0) after log10 transformation of LFQ intensities.ProteomicsRosa Lozano-DuránPARTIALDepartment of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, D-72076 Tübingen, GermanyNicotiana Benthamianairina.droste-borel@uni-tuebingen.de42755365 Zhou Y, Tan H, Giudicatti A, Vicente-Luque A, Weis M, Wehinger L, Schreidl M, Droste-Borel I, Macek B, Berendzen KW, Lozano-Durán R. Proteome profiling of plant Cajal bodies uncovers kingdom-specific components. Nucleic Acids Res. 2026 54(17):gkag867 10.1093/nar/gkag867Prof. Boris Macek Proteome Center Tuebingen University of Tuebingen Auf der Morgenstelle 15 72076 TuebingenGermanyMembraneless organelles (MLOs) in eukaryotic cells, such as the nuclear Cajal body (CB), have been notoriously difficult to biochemically isolate due to their dynamic and delicate nature. CBs, formed via liquid-liquid phase separation, mediate RNA processing and ribonucleoprotein assembly, essential for nuclear functions. In plants, this challenge has prevented any direct molecular characterization to date. Here, we report a successful isolation of plant CBs, achieved through a combination of biochemical purification and fluorescence-activated nuclei and particle sorting, enabling a previously unattainable biochemical access to this organelle. Mass spectrometry analysis defined a high-confidence set of plant CB-associated proteins, identifying 15 and 79 proteins uniquely localized and enriched in CBs, respectively, of which 18 are also labelled by CB markers in proximity labelling assays. While a partial overlap with known animal CB proteins exists, our data suggests a partially divergent composition of CB-associated proteins across kingdoms. This work breaks a major technical challenge, enabling detailed characterization of plant CBs and establishing a versatile platform adaptable for the isolation and molecular dissection of other MLOs.Proteome profiling of plant Cajal bodies uncovers kingdom-specific components.Zhou Yu Y, Tan Huang H, Giudicatti Axel A, Vicente-Luque Angela A, Weis Marvin M, Wehinger Lena L, Schreidl Marina M, Droste-Borel Irina I, Macek Boris B, Berendzen Kenneth Wayne KW, Lozano-Durán Rosa RfalseA plant Cajal body proteome reveals kingdom-specific componentsCajal bodies from Nicotiana benthamiana were isolated using fluorescence-activated particle sorting (FAPS) and subjected to LC-MS/MS for comprehensive proteomic profiling. In parallel, TurboID-based proximity labeling was performed using Cajal body-resident proteins to identify their proximal proteome.2026-09-212025-07-09PXD065938NEWT:6945NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:376741NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:1211601NEWT:876138NEWT:557436NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:1351NEWT:1438992NEWT:2649997NEWT:272563NEWT:79220NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:3885NEWT:3888NEWT:1589NEWT:135622NEWT:6915NEWT:3649NEWT:101510NEWT:3880NEWT:272559NEWT:3641NEWT:383379NEWT:10029NEWT:1000589NEWT:85963NEWT:85962NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:211586NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:197NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:1270NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:294128NEWT:11676NEWT:55571NEWT:100226NEWT:4530NEWT:4896NEWT:75058NEWT:13616NEWT:1094343NEWT:296543NEWT:1773NEWT:1895NEWT:1182590NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NCBITaxon:1313NEWT:43330NEWT:408169NEWT:44544NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:990119NEWT:408172NEWT:408170NEWT:493760NEWT:260710NEWT:257313NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:460519NEWT:1187947NEWT:1432138NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:9598NEWT:8030NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:432359NEWT:46835NEWT:2711NEWT:376686NEWT:95486NEWT:9103NEWT:29159NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:3635NEWT:5811NEWT:235443NEWT:272624NEWT:2719099NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:32644NEWT:499175NEWT:476272NEWT:3747NEWT:367830NEWT:178616NEWT:410289NEWT:373153NEWT:352472NEWT:360094NEWT:470NEWT:1313NEWT:411469NEWT:84023NEWT:559292NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2762NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:28038NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:327159NEWT:178876NEWT:327160NEWT:573NEWT:9031NEWT:7091NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:5180NEWT:256737NEWT:115104NEWT:1121114NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:13076NEWT:1249668NEWT:317NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:554NEWT:98334NEWT:426428NEWT:7574NEWT:7215NEWT:575412NEWT:29204NEWT:2172103NEWT:507601NCBITaxon:6157NEWT:746360NEWT:6239NEWT:470150NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NCBITaxon:2NEWT:985076NEWT:1215323NEWT:623NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:243230NEWT:8355NEWT:9685NEWT:7029NEWT:1080772NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:260707NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:105231NEWT:1216981NCBITaxon:6073NEWT:884204NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NEWT:607699NEWT:6282NEWT:426688NEWT:208964NEWT:1134506NEWT:575584NEWT:38783NEWT:8727NEWT:4006NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:5334NEWT:37334NEWT:382352NCBITaxon:10359NEWT:242619NEWT:632957NEWT:373995NEWT:5689NEWT:544404NEWT:9925NEWT:8839NEWT:4232NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:196627NEWT:5691NEWT:48479NEWT:627025NEWT:1097677NEWT:242507NEWT:61674NEWT:1117957NEWT:9913NEWT:4100NEWT:1076NEWT:6763NEWT:3498NEWT:803NEWT:29722NEWT:380394NEWT:1692259NEWT:180066NEWT:135588NEWT:1843183NEWT:58002NEWT:326423NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:1678078NEWT:749906NEWT:418985NEWT:146479NEWT:1911079NCBITaxon:620NEWT:264203NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:9612NEWT:38865NEWT:51953NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:349741NEWT:9605NEWT:9606NEWT:157295NEWT:641501NEWT:7668NEWT:915099NEWT:74940NEWT:9721NEWT:137221NEWT:1450511NEWT:1143193NEWT:411901NEWT:9838NEWT:105884NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:3055NEWT:58331NEWT:6326NEWT:6689NEWT:5476NEWT:1274432NEWT:1274426NEWT:70448NEWT:9825NEWT:1274423NEWT:393765NEWT:698936NEWT:39946NEWT:9823NEWT:9940NEWT:521001NEWT:39947NEWT:1274420NEWT:57845842755365