PXD046521 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Time-dependent proteomic signatures associated with embry-ogenic callus induction in Carica papaya L. |
Description | The cost of Carica papaya production through seed-based propagation is increased by sex segregation, making in vitro techniques a more appealing option for clonal propagation. Inducing embryogenic callus with 2,4-dichlorophenoxyacetic acid (2,4-D) hold the potential to large-scale cloning, although the molecular mechanisms underlying this process are still not well understood. In this study, we performed a temporal analysis in the proteome of C. papaya callus to identify the key players involved in embryogenic differentiation. Mature zygotic embryos were used as explants and treated with 20 μM 2,4-D to induce embryogenic callus. Total proteins were extracted at 0, 7, 14, and 21 days (T0, T7, T14, and T21), and 1407 proteins were identified using bottom-up proteomic approach. Comparative proteomics revealed 957 differentially accumulated proteins (DAPs) (p<0.05 and log2FC >0.585 or <-0.585) in at least one comparison between the analyzed induction times points. The clustering analysis revealed four clusters with distinct patterns of protein accumulation throughout the embryogenic callus induction treatment. The cluster 1 contains 386 DAPs that accumulated at all analyzed times after treatment with 2,4-D. In contrast, cluster 2 contains 165 DAPs that decrease in abundance during the induction. The cluster 3 contains 251 proteins that are most abundant just after the start of incubation in 2,4-D (T7) and cluster 4 grouped 155 proteins that accumulate after callus formation. Functional analysis revealed that proteins involved with reserve storage and seed maturation were more abundant in the explant at T0 and decreased as callus formation progressed. Biological processes involving carbohydrate and amino acid metabolism, aerobic respiration, and protein catabolic processes were enriched after induction treatment. Regulatory proteins, including histone deacetylase (HDT3) and argonaute 1, were more abundant after the start of induction treatment with 2,4-D, suggesting their role in acquisition of embryogenic competence. Predicted protein-protein networks revealed the regulatory role of proteins 14.3.3 accumulated during callus induction and the association of proteins involved in oxidative phosphorylation, hormone response, and SAM metabolism. Our findings emphasize the modulation of the proteome at different stages during embryogenic callus initiation and identify regulatory proteins that might be involved with the activation of this process. |
HostingRepository | PRIDE |
AnnounceDate | 2024-01-26 |
AnnouncementXML | Submission_2024-01-26_08:22:38.499.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Vanildo Silveira |
SpeciesList | scientific name: Carica papaya; NCBI TaxID: 3649; |
ModificationList | No PTMs are included in the dataset |
Instrument | SYNAPT G2-Si |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-10-30 21:40:42 | ID requested | |
⏵ 1 | 2024-01-26 08:22:39 | announced | |
Publication List
Xavier LR, Corr, ê, a CCG, da Paschoa RP, Vieira KDS, Pacheco DDR, Gomes LDES, Duncan BC, da Concei, ç, ã, o LDS, Pinto VB, Santa-Catarina C, Silveira V, L. Plants (Basel), 12(22):(2023) [pubmed] |
10.3390/plants12223891; |
Keyword List
submitter keyword: Bottom-up proteomics |
Carica papaya |
Embryogenic callus |
Somatic embryos |
Time-series analysis. |
Contact List
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 | |
Full Dataset Link List
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/2024/01/PXD046521 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD046521
- Label: PRIDE project
- Name: Time-dependent proteomic signatures associated with embry-ogenic callus induction in Carica papaya L.