PXD027388-2

PXD027388 is an original dataset announced via ProteomeXchange.

Title	Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in maintenance and expression of embryogenic competence in sugarcane callus
Description	Sugarcane (Saccharum spp.) is one of the most important crops for sugar, biofuels and bioenergy production, becoming an important commodity in the world agricultural market for more than 100 countries. In this study, label-free quantitative proteomics and phosphoproteomics analyses were performed to investigate signaling events related to somatic embryo maturation and differentiation in sugarcane. Embryogenic callus (EC) at the multiplication (EC0) and after 14 days (EC14) under maturation were compared. A total of 251 phosphoproteins and 700 proteins were differentially regulated and accumulated, respectively, in the EC14/EC0 comparison. Metabolic pathways analysis showed that proteins and phosphoproteins are enriched in lysine degradation and starch/sucrose metabolism during multiplication, while differentiation of somatic embryo involves the regulation of energetic metabolism, including TCA cycle, oxidative phosphorylation, and carbon metabolism. Multiplication-related phosphoproteins were mainly associated to abscisic acid responses and transcriptional regulation comprising the TOPLESS (TPL), SNF1 kinase homolog 10 (KIN10), SEUSS (SEU), and LEUNIG_HOMOLOG (LUH) proteins. In maturation-related phosphoproteins, the phosphorylation of the proteins light harvesting complex photosystem ii, CURVATURE THYLAKOID 1B, vacuolar proton ATPase A1 and phytochrome interacting factor 3-LIKE 5 is associated to bioenergetic metabolism and carbon fixation. Motif analysis revealed 15 phosphorylation motifs, of which the [D-pS / T-x-D] motif was unique for the phosphopeptides identified during somatic embryo differentiation. Co-expression network analysis of proteins and phosphoproteins revealed the interaction between SNF1-related protein kinase 2 (SnRK2), abscisic acid responsive elements-binding factor 2 (ABF2), and KIN10, indicating the role of these proteins in the embryogenic competence in EC0. The interactions between ubiquitin-conjugating enzyme 5, ubiquitin-conjugating enzyme 35, small ubiquitin-like modifier 1, and histone deacetylase 1 may be involved in post-translational protein modification during the embryo maturation stage. argonaute 1 (AGO1) also interacts with POLTERGEIST (POL) and may integrate gene silencing and regulation of meristem identity during somatic embryo development. These results reveal novel dynamics of protein regulation in somatic embryogenesis and identify new potential players in somatic embryo differentiation and their phosphosites.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:53:04.596.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: 193079;
ModificationList	phosphorylated residue
Instrument	timsTOF Pro; SYNAPT G2-Si

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-18 23:37:46	ID requested
1	2022-05-07 11:48:01	announced
⏵ 2	2023-11-14 08:53:05	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: label-free phosphoproteomics, embryo development,somatic embryogenesis, sugarcane

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/2022/05/PXD027388

PRIDE project URI

• PRIDE
  1. PXD027388
     1. Label: PRIDE project
     2. Name: Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in maintenance and expression of embryogenic competence in sugarcane callus