PXD062095

PXD062095 is an original dataset announced via ProteomeXchange.

Title	Proteomic and Phosphoproteomic Analyses during Plant Regeneration Initiation in Cotton (Gossypium hirsutum L.)
Description	Somatic embryogenesis (SE) is a biotechnological tool used to generate new individuals and is the preferred method for rapid plant regeneration. However, the molecular basis underlying somatic cell regeneration through SE is not yet fully understood, particularly regarding interactions between the proteome and post-translational modifications. Here, we performed association analysis of high-throughput proteomics and phosphoproteomics in three representative samples (non-embryogenic calli, NEC; primary embryogenic calli, PEC; globular embryos, GE) during the initiation of plant regeneration in cotton, a pioneer crop for genetic biotechnology applications. Our results showed that protein accumulation is positively regulated by phosphorylation during SE, as revealed by correlation analyses. Of the 1418 proteins that were differentially accumulated in the proteome and the 1106 phosphoproteins that were differentially regulated in the phosphoproteome, 115 proteins with 229 phosphorylation sites overlapped (co-differential). Furthermore, seven dynamic trajectory patterns of differentially accumulated proteins (DAPs) and the correlated differentially regulated phosphoproteins (DRPPs) pairs with enrichment features were observed. During the initiation of plant regeneration, functional enrichment analysis revealed that the overlapping proteins (DAPs-DRPPs) were considerably enriched in cellular nitrogen metabolism, spliceosome formation, and reproductive structure development. Moreover, 198 DRPPs (387 phosphorylation sites) were specifically regulated at the phosphorylation level and showed four patterns of stage-enriched phosphorylation susceptibility. Furthermore, enrichment annotation analysis revealed that these phosphoproteins were significantly enriched in endosomal transport and nucleus organization processes. During embryogenic differentiation, we identified five DAPs-DRPPs with significantly enriched characteristic patterns. These proteins may play essential roles in transcriptional regulation and signaling events that initiate plant regeneration through protein accumulation and/or phosphorylation modification. This study enriched the understanding of key proteins and their correlated phosphorylation patterns during plant regeneration, and also provided a reference for improving plant regeneration efficiency.
HostingRepository	PRIDE
AnnounceDate	2025-03-21
AnnouncementXML	Submission_2025-03-20_20:28:17.450.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Huihui Guo
SpeciesList	scientific name: Gossypium hirsutum; NCBI TaxID: 3635;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-20 19:29:17	ID requested
⏵ 1	2025-03-20 20:28:17	announced

10.3390/GENES15081079;

submitter keyword: Proteomic and phosphoproteomic analyses

Somatic embryogenesis

Plant regeneration

Cotton

Haixia Guo, Jin Wang, Xuehui Huo, Xiwang Cui, Li Zhang, Xiushan Qi, Xiaoying Wu, Junchen Liu, Aijuan Wang, Jialin Liu, Xiangyu Chen, Fanchang Zeng and Huihui Guo
contact affiliation	Shandong Agricultural University
contact email	hhguo@sdau.edu.cn
lab head
Huihui Guo
contact affiliation	Shandong Agricultural University
contact email	hhguo@sdau.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062095
     1. Label: PRIDE project
     2. Name: Proteomic and Phosphoproteomic Analyses during Plant Regeneration Initiation in Cotton (Gossypium hirsutum L.)