Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/protein_quantification_report.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/peptide_quantification_report.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_A3.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_B1.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_AB3.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_C1.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_A1_B.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_B3.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_AB2.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_B2.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_AB1.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_C3.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_C2.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/2024_08_15_Clicia_Milho_A2.raw.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/OUTPUT_PLGS.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098/ROOT.zipprimaryOK200cgrativol@uenf.brClicia GrativolMass SpectrometryData-independent acquisitionBottom-up proteomicsNot availablemicrobiome.dna hypomethylationPlant-microorganism interactionPlant-microorganism interaction; dna hypomethylation; epigenetic regulation; 5-azacitidine; microbiome.5-azacitidineepigenetic regulationhttps://www.ebi.ac.uk/pride/archive/projects/PXD077098Plant CellRootProtein extraction Roots from maize seedlings were treated with the methylation inhibitor 5-azaC for 7 days and/or inoculated with H. seropedicae during the last 48 hours of the same period. Treatments included Control, Bacteria, 5-azaC, and 5-azaC+Bacteria. After seven days of growth, roots were macerated in liquid nitrogen. Three biological replicates (300 mg fresh mass each) were used for protein extraction. Each replicate was mixed with 1 mL of extraction buffer containing 10% TCA/acetone and 20 mM dithiothreitol. Protein concentration was determined using the Bradford Protein Assay Kit with bovine gamma globulin as standard. Protein digestion For the protein digestion, 100 µg of extracted proteins from each biological replicate were precipitated using the methanol/chloroform method to remove any interference from the samples before digestion with trypsin (Nanjo et al. 2012). After the protein precipitation, the samples were resuspended in a 7 M urea/2 M thiourea solution for proper suspension. Tryptic protein digestion (1:100 enzyme:protein) was performed using the filter-aid sample preparation (FASP) (Wiśniewski et al. 2009), with modifications. Protein aliquots were added to the Microcon-30 kDa filter units (Lipecka et al. 2016), washed with 200 µl of 50 mM ammonium bicarbonate (solution A) and centrifuged at 10,000g for 15 min at 25°C (unless stated otherwise, all centrifugation steps were performed under this condition). This step was repeated once for complete removal of urea before protein reduction. Afterwards, 100 µL of 50 mM DTT, freshly made in solution A, was added, vortexed and incubated for 20 min at 60°C. Then, 200 µl of 8 M urea in 50 mM ammonium bicarbonate (solution B) was added, and centrifuged for 15 min. For protein alkylation, 100 µL of 50 mM iodoacetamide freshly prepared in solution B, was added, gently vortexed and incubated for 20 min at 25°C in the absence of light (1 min agitation and 19 min resting, at 47 g). Next, 200 µl of solution B was added and centrifuged for 15 min. This step was repeated once. Then, 200 µl of solution A was added and centrifuged for 15 min. This step was repeated twice. Approximately 50 µl of the sample should remain in the last washing. For protein digestion, 25 µl of 0.2% (v/v) RapiGest and 25 µl of trypsin solution were added, gently vortexed and incubated for 18 h at 37°C (1 min agitation and 4 min resting at 47 g). For peptide elution, the filter units were transferred to new microtubes and centrifuged for 10 min, then 50 µl of solution A was added and centrifuged for 15 min. This step was repeated once. For RapiGest precipitation and trypsin inhibition, 5 µl of 15% trifluoroacetic acid (TFA) was added, gently vortexed and incubated for 30 min at 37°C. Then, samples were centrifuged for 15 min and the supernatants were collected and vacuum dried. The peptides were resuspended in 100 µl of a solution 95% 50 mM ammonium bicarbonate, 5% acetonitrile and 0.1% formic acid. The resulting peptides were quantified by the A205 nm protein and peptide method, using a NanoDrop 2000C spectrophotometer. Mass spectrometry analyses Mass spectrometry was performed using a nanoACQUITY ultraperformance liquid chromatograph (UPLC) coupled to a Q-TOF SYNAPT G2-Si instrument. Runs consisted of three biological replicates of 1 μg of digested peptides. During separation, the samples were loaded onto a nanoACQUITY UPLC M-Class Symmetry C18 5 μm trap column (180 μm × 20 mm) at 5 μL min-1 for 3 min and then onto a nanoACQUITY M-Class HSS T3 1.8 μm analytical reversed-phase column (75 μm × 150 mm) at 400 nL min-1, with a column temperature of 45ºC. For peptide elution, a binary gradient was used, with mobile phase A consisting of water and 0.1% formic acid, and mobile phase B consisting of acetonitrile and 0.1% formic acid. Gradient elution started with 5% B, which then increased from 5 to 40% B until 91.12 min, and from 40 to 99% B until 95.12 min, after which it was maintained at 99% until 99.12 min. The elution then decreased to 5% B until 101.12 min, after which it was maintained at 5% B until the end of the run at 117.00 min. Mass spectrometry was performed in positive and resolution mode (V mode) at 35,000 FWHM with ion mobility (HDMSE) and in data-independent acquisition (DIA) mode, with the ion mobility wave velocity program starting at 800 m s-1 and ending at 500 m s-1. The transfer collision energy increased from 25 to 55 V in high-energy mode, the cone and capillary voltages were 40 and 2,800 V, respectively, the pressure of the nano-flow gas was 0.5 bar, the purge gas flow rate was 150 L h-1, and the source temperature was 100ºC. For the time-of-flight (TOF) parameters, the scan time was set to 0.6 s in continuous mode, with a mass range of 50 to 2,000 Da. Human [Glu1]-fibrinopeptide B at 100 fmol μL-1 was used as an external calibrant, and lock mass acquisition was performed every 30 s. Mass spectra were subsequently acquired by MassLynx v4.0 software.PrideNot availableSpectral processing and database searching were performed using ProteinLynx Global Server (PLGS; v3.0.2; Waters) and ISOQuant workflow software (Distler et al. 2014; 2016). The spectra were processed by PLGS using a low-energy threshold of 150 (counts), an elevated energy threshold of 50, and an intensity threshold of 750. In addition, the analysis was performed using the following parameters: two missed cleavages, a minimum fragment ion per peptide equal to 3, a minimum fragment ion per protein equal to 7, a minimum peptide per protein equal to 2, fixed modifications of carbamidomethyl, and variable modifications of oxidation and phosphoryl. The false discovery rate (FDR) for peptide and protein identification was set to a maximum of 1%, with a minimum peptide length of six amino acids. The proteomic data were processed against the information of the Zea mays protein databank from https://phytozome-next.jgi.doe.gov/info/Zmays_Zm_B73_REFERENCE_NAM_5_0_55. The comparative label-free quantification analysis was performed using the ISOQuant software, by using previously described settings and algorithms (Distler et al. 2014; 2016). Briefly, the analysis included retention time alignment, exact mass retention time and ion mobility spectrometry clustering as well as data normalization and protein homology filtering. ISOQuant annotates the resulting feature clusters by evaluating consensus peptide identifications and identification probabilities. Protein identification parameters in ISOQuant were set to a false discovery rate of 1%, a peptide score greater than six, a minimum peptide length of six amino acids, and at least two peptides per protein. Label-free quantification was estimated using the TOP3 quantification approach, followed by the multidimensional normalization process implemented within ISOQuant (Distler et al. 2014). After ISOQuant analysis, only the proteins that were either present or absent (for unique proteins) in all three biological replicates of each comparison were considered for differential abundance analysis. Data were analyzed using Student’s t-test (two-tailed). Proteins with p-values lower than 0.05 were considered up-accumulated if the log2 of fold change was greater than 0.6, and down-regulated if the log2 of the fold change was lower than -0.6. Finally, for functional annotation, the differentially regulated proteins were blasted against the non-redundant (nr) plants/viridiplantae_protein_sequences database using the OmicsBox software (Blast2Go).ProteomicsClicia Grativol Gaspar de MatosUniversidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Centro de Biociências e Biotecnologia, Laboratório de Química e Função de Proteínas e Peptídeos, Prédio P5, Sala 228, Bairro Parque Califórnia, Campos dos Goytacazes, RS - CEP: 28013-602PARTIALZea Mays (maize)cgrativol@uenf.br42017455 Zocateli PI, de Olímpio GV, de Almeida FA, da Rocha LO, de Sena Martins DV, Sangi S, Olivares FL, de Matos EM, Siqueira J, Viccini LF, da Paschoa RP, Silveira V, Grativol C. DNA Methylation Shapes Seed-Borne Microbiome and Proteome Responses During Early Maize-Beneficial Bacteria Interactions. Plant Cell Environ. 2026 10.1111/pce.70552Universidade Estadual do Norte FluminenseBrazilMicroorganism and plant interactions are crucial for development and environmental adaptation. Plant growth promoting bacteria enhance agricultural productivity in a sustainable manner, while epigenetic modifications such as DNA methylation regulate gene expression and adaptive responses. The objective of this study is to determine how DNA hypomethylation influences early interactions between maize (Zea mays) and the endophytic diazotrophic bacterium Herbaspirillum seropedicae, particularly regarding plant growth, metabolism, and the root microbiome. Treatment with the hypomethylating agent 5-azacytidine (5-azaC) altered maize root morphology without affecting bacterial growth. Inoculation with H. seropedicae promoted plant growth and bacterial colonisation in root mucilage, with higher accumulation in 5-azaC treated roots. Global methylation analysis showed that bacterial inoculation modulates cytosine methylation in a manner similar to 5-azaC, suggesting a role in epigenetic regulation. Gene expression analysis of DNA methylation machinery confirmed that hypomethylation drives plant-microbe interactions. Root microbiome profiling revealed that 5-azaC disrupted microbial composition, which was partially restored by bacterial inoculation. Proteomic analysis identified 1,818 proteins and highlighted significant changes in metabolic pathways, especially carbon metabolism and the citric acid cycle. These findings demonstrate that DNA hypomethylation combined with bacterial interaction profoundly affects cellular and metabolic processes and provide insights for sustainable agricultural practices through epigenetic and microbial modulation.DNA Methylation Shapes Seed-Borne Microbiome and Proteome Responses During Early Maize-Beneficial Bacteria Interactions.Zocateli Pedro Igor PI, Olímpio Geovanna Vitória GV, de Almeida Felipe Astolpho FA, da Rocha Letícia Oliveira LO, de Sena Martins Diego Vinicius DV, Sangi Sara S, Olivares Fábio Lopes FL, de Matos Elyabe Monteiro EM, Siqueira Juliana J, Viccini Lyderson Facio LF, da Paschoa Roberta Pena RP, Silveira Vanildo V, Grativol Clícia CfalseDNA methylation shapes seed-borne microbiome and proteome responses during early maize-beneficial bacteria interactionsProject Description: The interaction between microorganisms and plants plays a key role in plant development and environmental adaptation. Among these microorganisms, plant growth-promoting bacteria (PGPB) enhance agricultural productivity sustainably. Beyond direct effects on plant physiology, epigenetic modifications such as DNA methylation regulate gene expression and adaptive responses. This study investigates how DNA hypomethylation influences early interactions between maize (Zea mays) and the PGPB Herbaspirillum seropedicae, focusing on plant growth, metabolism, and root microbiome. Treatment with the hypomethylating agent 5-azacytidine (5-azaC) did not affect bacterial growth but induced notable phenotypic changes in maize, particularly in root morphology. Inoculation with H. seropedicae enhanced plant growth across biometric parameters. Microscopy revealed bacterial colonization primarily in root mucilage, with higher bacterial accumulation in 5-azaC-treated roots. Global methylation analysis indicated that H. seropedicae modulates cytosine methylation similarly to 5-azaC, suggesting a role in epigenetic regulation. Gene expression analysis of DNA methylation machinery supports hypomethylation as a driver of plant-microbe interactions. Root microbiome profiling showed that 5-azaC significantly altered microbial composition, whereas bacterial inoculation partially restored it toward control profiles. Proteomic analysis identified 1,818 proteins, highlighting significant shifts in metabolic pathways, especially carbon metabolism and the citric acid cycle. These findings demonstrate that DNA hypomethylation, combined with bacterial interaction, profoundly impacts cellular and metabolic processes, offering new insights into early plant-microbe interactions. This knowledge may contribute to developing sustainable agricultural practices through epigenetic and microbial modulation.2026-05-052026-04-14PXD077098NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:43186NEWT:428146NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:1401257NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:145458NEWT:633149NEWT:1149786NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:1772NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:1245466NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NEWT:272634NEWT:198107NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT:9534NEWT:6269NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:208893NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:377586NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:9793NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:27457NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:419610NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCB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