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PotesilMass SpectrometryBottom-up proteomicsP-bodiesEif4aRna condensationMeiotic bodiesEif4fMeiosisRnp granulesStress granulesBiomolecular condensatesSmg7https://www.ebi.ac.uk/pride/archive/projects/PXD061406FlowerIn-gel digestion The immunoprecipitated proteins were separated using 1D-SDS-PAGE gel electrophoresis (12% gel, one replicate per gel) and whole gel lanes selected for analysis were excised in the form of bands (30 bands per lane). After destaining and washing procedures, each band was washed by 50% ACN/NaHCO3 and pure ACN and the gel pieces were incubated with 125 ng trypsin (sequencing grade; Promega) in 50mM NaHCO3. The digestion was performed for 2 h at 40 °C on a Thermomixer (750 rpm; Eppendorf). Tryptic peptides were extracted info LC-MS vials by 2.5% formic acid (FA) in 50% ACN with addition of polyethylene glycol (20,000; final concentration 0.001%) and concentrated in a SpeedVac concentrator (Thermo Fisher Scientific). LC-MS/MS analysis of peptides after in-gel digestion LC-MS/MS analyses of individual gel band digests were done using RSLCnano system connected to Orbitrap Elite hybrid spectrometer (Thermo Fisher Scientific). Prior to LC separation, tryptic digests were online concentrated and desalted using trapping column (100 μm × 30 mm) filled with 3.5-μm X-Bridge BEH 130 C18 sorbent (Waters). After washing of trapping column with 0.1% FA, the peptides were eluted (flow 300 nl/min) from the trapping column onto a Acclaim Pepmap100 C18 column (2 µm particles, 75 μm × 250 mm; Thermo Fisher Scientific) by the following gradient program (mobile phase A: 0.1% FA in water; mobile phase B: 80% ACN containing 0.1% FA): the gradient elution started at 1% of mobile phase B and increased from 1% to 56% during the first 50 min (1% in the 1st, 30% in the 30th and 56% in 50th min), then increased linearly to 80% of mobile phase B in the next 5 min and remained at this state for the next 10 min. Equilibration of the trapping column and the column was done prior to sample injection to sample loop. The analytical column outlet was directly connected to the Nanospray Flex Ion Source (Thermo Fisher Scientific). MS data were acquired in a data-dependent strategy selecting up to top 10 precursors based on precursor abundance in the survey scan (350-2000 m/z). The resolution of the survey scan was 60,000 (400 m/z) with a target value of 1×106 ions, one microscan and maximum injection time of 200 ms. HCD MS/MS spectra (relative fragmentation energy of 32 %, resolution 15,000 at 400 m/z) were acquired with a target value of 50 000 ions with m/z range adjusted according to actual precursor mass and charge. The maximum injection time for MS/MS was 500 ms. Dynamic exclusion was enabled for 45 s after one MS/MS spectra acquisition and early expiration was disabled. The isolation window for MS/MS precursor isolation was set to 2 m/z.PrideNot availableFor data evaluation, MaxQuant software (v1.6.17.0) (Cox J, Mann M. 2008) with inbuild Andromeda search engine (Cox J et al 2011) was used. Search was done against protein databases of Arabidopsis thaliana (27,469 protein sequences, version from 2021-11-17, downloaded from: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000006548/UP000006548_3702.fasta.gz) and cRAP contaminants (112 sequences, version from 2018-11-22, downloaded from http://www.thegpm.org/crap). The following variable modifications were set for the database search: oxidation (M), propionamide (C), and acetylation (Protein N-term). Enzyme specificity was tryptic with two permissible miscleavages. Only peptides and proteins with false discovery rate threshold under 0.01 were considered. Relative protein abundance was assessed using protein intensities calculated by MaxQuant. Match between runs was enabled and set using the fractions scheme specifying individual bands as different consecutive fractions (1-30) using the same fraction number for the corresponding gel area from the two samples of one replicate but different fraction number between replicates.ProteomicsZbynek ZdrahalProteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech RepublicCOMPLETEArabidopsis Thaliana (mouse-ear Cress)david.potesil@ceitec.muni.czNot availableProteomics Core Facility and Research Group Proteomics CEITEC-MU Masaryk University Brno, Czech RepublicCzech Republic10.6019/PXD061406falseA SMG7-eIF4A module constitutes a homeostatic system for P-bodies and Meiotic bodiesThe nucleation of RNP granules requires the participation of mRNAs, which simultaneously as becoming their target, dictate their properties. Here we report that in Arabidopsis the RNA helicase eIF4A limits the condensation of P-bodies acting as an RNA chaperone, disassembled from the eIF4F complex. eIF4A is recruited into P-bodies by SMG7, previously known to recruit UPF1 and TDM1. In response to heat shock (HS) eIF4A shares distribution within stress granules (SGs) and P-bodies, modulating the condensation of both RNP granules. Our study of meiotic RNP granules demonstrates the nucleation of the meiotic body (M-body), constituted by a P-body core and a SGs surrounding shell. SMG7 recruits eIF4A in the M-body core to modulate its condensation, which impacts the functionality of this body an influence plant reproduction. We conclude that SMG7 governs the functionality of P-bodies and M-bodies, and with eIF4A, constitutes a homeostatic system to control their level of condensation2026-03-252025-03-03PXD061406NEWT:6945NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:1211601NEWT:876138NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:1351NEWT:1438992NEWT:2649997NEWT:272563NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:3885NEWT:3888NEWT:1589NEWT:135622NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:3880NEWT:272559NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:1000589NEWT:85963NEWT:85962NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:197NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:1270NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:286NEWT: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:3712NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:243277NEWT: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:1182263NEWT:2711NEWT:376686NEWT:95486NEWT:9103NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:3635NEWT:5811NEWT:235443NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:32644NEWT:225117NEWT:499175NEWT:109779NEWT:476272NEWT:3747NEWT:195051NEWT:367830NEWT:1255228NEWT:178616NEWT:410289NEWT:373153NEWT:352472NEWT:357NEWT:360094NEWT:470NEWT:1313NEWT:411469NEWT:84023NEWT:559292NEWT:39491NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:327159NEWT:178876NEWT:327160NEWT:573NEWT:9031NEWT:7091NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:5180NEWT:256737NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1249668NEWT:317NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:554NEWT:98334NEWT:426428NEWT:7574NEWT:1715256NEWT:7215NEWT:575412NEWT:29204NEWT:2172103NEWT:507601NEWT:643680NCBITaxon:6157NEWT:746360NEWT:6239NEWT:470150NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NCBITaxon:2NEWT:985076NEWT:1215323NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:243230NEWT:8355NEWT:9685NEWT:7029NEWT:1080772NEWT:8479NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:260707NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:105231NCBITaxon:6073NEWT:884204NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NEWT:607699NEWT:6282NEWT:208964NEWT:1134506NEWT:575584NEWT:38783NEWT:8727NEWT:4006NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:5334NEWT:37334NEWT:382352NCBITaxon:10359NEWT:242619NEWT:632957NEWT:34073NEWT:373995NEWT:544404NEWT:9925NEWT:8839NEWT:4232NEWT:2758385NEWT:37349NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:196627NEWT:5691NEWT:48479NEWT:627025NEWT:1097677NEWT:61674NEWT:1117957NEWT:9913NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:29722NEWT:380394NEWT:1692259NEWT:180066NEWT:135588NEWT:1843183NEWT:58002NEWT:326423NEWT:36111NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:1678078NEWT:749906NEWT:418985NEWT:146479NEWT:1911079NEWT:69373NEWT:264203NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:9612NEWT:38865NEWT:51953NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:1355477NEWT:349741NEWT:9605NEWT:9606NEWT:90371NEWT:157295NEWT:641501NEWT:7668NEWT:915099NEWT:74940NEWT:9721NEWT:137221NEWT:9600NEWT:1450511NEWT:1143193NEWT:411901NEWT:9838NEWT:105884NCBITaxon:9615NEWT:9839NEWT:58334NEWT:1193501NEWT:3055NEWT:58331NEWT:6326NEWT:6689NEWT:5476NEWT:299767NEWT:1274432NEWT:1274426NEWT:70448NEWT:9825NEWT:1274423NEWT:393765NEWT:698936NEWT:39946NEWT:9823NEWT:9940NEWT:521001NEWT:39947NEWT:1274420NEWT:5784580000-0003-0390-0904