PXD077098

PXD077098 is an original dataset announced via ProteomeXchange.

Title	DNA methylation shapes seed-borne microbiome and proteome responses during early maize-beneficial bacteria interactions
Description	Project 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.
HostingRepository	PRIDE
AnnounceDate	2026-05-05
AnnouncementXML	Submission_2026-05-05_10:40:32.255.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Clicia Grativol
SpeciesList	scientific name: Zea mays (Maize); NCBI TaxID: NEWT:4577;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2026-04-13 18:02:42	ID requested
⏵ 1	2026-05-05 10:40:34	announced

10.1111/pce.70552;

Zocateli PI, Ol, í, mpio 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) [pubmed]

submitter keyword: Plant-microorganism interaction

DNA hypomethylation

Epigenetic regulation

5-azacitidine

Microbiome.

Clicia Grativol Gaspar de Matos
contact affiliation	Universidade 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: 28013-602
contact email	cgrativol@uenf.br
lab head
Clicia Grativol
contact affiliation	Universidade Estadual do Norte Fluminense
contact email	cgrativol@uenf.br
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077098

PRIDE project URI

• PRIDE
  1. PXD077098
     1. Label: PRIDE project
     2. Name: DNA methylation shapes seed-borne microbiome and proteome responses during early maize-beneficial bacteria interactions