PXD068502-1

PXD068502 is an original dataset announced via ProteomeXchange.

Title	Early regulatory networks driving somatic embryogenesis in Saccharum spp. L. revealed by time-resolved proteomics
Description	Sugarcane (Saccharum spp. hybrid) is an economically important crop that is widely grown for its sucrose content, and somatic embryogenesis is a promising approach for efficient micropropagation and genetic transformation in this context. The induction of somatic embryogenesis is controlled by various genes and proteins involved in hormonal pathways and stress responses, which act as key regulators of in vitro cellular reprogramming. In this study, we employed a temporal proteomic approach to investigate the underlying molecular mechanisms governing sugarcane embryogenic callus formation in response to 2,4-dichlorophenoxyacetic acid (2,4-D) during induction. Comprehensive proteomic profiling revealed 996 differentially accumulated proteins (DAPs) across at least one pairwise comparison among time points (0, 7, 14 and 21 days) during callus induction. These DAPs were classified into different clusters on the basis of their accumulation profile. Our study advances the understanding of the molecular mechanisms of somatic embryogenesis in sugarcane, highlighting the regulation of key proteins during this process. Proteins involved in photosynthesis and starch accumulation were not detected during callus induction. In contrast, proteins involved in embryogenesis, histone epigenetic regulation, hormone responses and protein post-translational modification accumulate during callus induction. The predicted interactions between the TOPLESS protein and auxin response proteins (SKP1, CUL1 and CAND1 proteins) are associated with increased accumulation of the histone deacetylase HDT2 protein, a regulator of chromatin condensation, during embryogenic callus initiation. Moreover, proteomic analysis revealed a temporal reduction in methylation cycle enzymes during callus induction, whereas global DNA methylation (GDM) showed only a slight, non-significant increase, suggesting that additional regulatory layers are involved in embryogenic competence. The identified protein dynamics provide valuable targets for refining somatic embryogenesis protocols and advancing their biotechnological applications in sugarcane.
HostingRepository	PRIDE
AnnounceDate	2026-01-15
AnnouncementXML	Submission_2026-01-14_21:57:32.159.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vanildo Silveira
SpeciesList	scientific name: Saccharum hybrid cultivar SP80-3280; NCBI TaxID: NEWT:193079;
ModificationList	No PTMs are included in the dataset
Instrument	SYNAPT G2-Si

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-18 14:43:16	ID requested
⏵ 1	2026-01-14 21:57:32	announced

10.1016/J.JPROT.2026.105602;

submitter keyword: Embryogenic callus induction

proteomics

somatic embryogenesis

DNA methylation

cell totipotency.

Vanildo Silveira
contact affiliation	Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, Campos dos Goytacazes, RJ, Brazil. Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Campos dos Goytacazes, RJ, Brazil.
contact email	vanildo@uenf.br
lab head
Vanildo Silveira
contact affiliation	UNIVERSIDADE ESTADUAL DO NORTE FLUMINENSE
contact email	vanildo@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/2026/01/PXD068502

PRIDE project URI

• PRIDE
  1. PXD068502
     1. Label: PRIDE project
     2. Name: Early regulatory networks driving somatic embryogenesis in Saccharum spp. L. revealed by time-resolved proteomics