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Proteomes and Ubiquitylomes Analysis in rosa hybrida during petal abscission.

ABSTRACT: The ubiquitome dataset by imputing missing values and normalization of 6844 ubiquitin modified peptides, 7026 lysine ubiquitination (Kub) site were defined in 2720 proteins, of which 3718 Kub site in 1379 proteins were quantified. Among these quantified Kub sites and proteins, 139 sites in 100 proteins were identified as upregulated ubiquitination sites, and 55 sites in 48 proteins were identified as downregulated ubiquitination sites at a threshold of 1.5 (P < 0.05)

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Rosa Chinensis

TISSUE(S): Abscission Zone

SUBMITTER: Chuyan Jiang

LAB HEAD: Chao Ma

PROVIDER: PXD036672 | Pride | 2023-03-11

REPOSITORIES: Pride

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			Action	DRS
	F9233LPUb_stage3_1_Slot1-45_1_1231.d.zip	Other
	F9233LPUb_stage3_2_Slot1-46_1_1233.d.zip	Other
	F9233LPUb_stage3_3_Slot1-47_1_1235.d.zip	Other
	F9233LPUb_stage5_1_Slot1-48_1_1237.d.zip	Other
	F9233LPUb_stage5_2_Slot1-49_1_1239.d.zip	Other

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Publications

Integrative analysis of transcriptome, proteome, and ubiquitome changes during rose petal abscission.

Jiang Chuyan C Jiang Tianhua T Deng Shuning S Yuan Chaoli C Liang Yue Y Li Susu S Ma Chao C Gao Yuerong Y

Frontiers in plant science 20221019

Plant organ abscission is regulated by multiple physiological and biochemical processes. However, the transcriptional, translational, and post-translational modifications occurring during organ abscission have not been systematically investigated. In this study, we report transcriptome, proteome, and ubiquitome data for the abscission zone (AZ) of rose petals collected during petal shedding. We quantified 40,506 genes, 6,595 proteins, and 2,720 ubiquitinated proteins in rose petal AZ. Our result ...[more]

PMID: 36340335

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Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation in rosa hybrida during petal abscission.

Project description:We employed Non-standard quantitative techniques and quantitative proteomics techniques based on mass spectrometry to perform proteomics analyses for the petal abscission zone of rose petal at stage 3 stage 5. In total, 6595 proteins were detected, we compared differentially expressed proteins (DEPs) between stage 3 and stage 5 (FC>1.5, P-value<0.05). We found that 271 proteins were significantly up-regulated, while 444 proteins were significantly down-regulated.

2023-03-11 | PXD036665 | Pride

Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation

Project description:Petal senescence is a complex programmed process. It has been previously demonstrated that treatment with ethylene, a plant hormone involved in senescence, can extensively alter transcriptome and proteome profiles in plants. However, little is known regarding the impact of ethylene on post-translational modification (PTM) or the association between PTM and the proteome. Protein degradation is one of the hallmarks of senescence, and ubiquitination, a major PTM in eukaryotes, plays important roles in protein degradation. In this study, we first obtained reference petunia transcriptome data via RNA sequencing. Next, we quantitatively investigated the petunia proteome, ubiquitylome, and the association between them in petunia corollas following ethylene treatment. In total, 51,799 unigenes, 3,606 proteins, and 2,270 ubiquitination sites were quantified 16 hours after ethylene treatment. Treatment with ethylene resulted in 14,448 down-regulated and 6,303 up-regulated unigenes (absolute log2-fold change >1 and FDR<0.001), 284 down-regulated and 233 up-regulated proteins, and 320 up-regulated and 127 down-regulated ubiquitination sites using a 1.5-fold threshold (P<0.05), indicating that global ubiquitination levels increase during ethylene-mediated corolla senescence in petunia. Several putative ubiquitin ligases were up-regulated at the protein and transcription levels. Our results showed that the global proteome and ubiquitylome were negatively correlated and that ubiquitination could be involved in the degradation of proteins during ethylene-mediated corolla senescence in petunias. Ethylene regulates hormone signaling transduction pathways at both the protein and ubiquitination levels in petunia corollas. In addition, our results revealed that ethylene increases the ubiquitination levels of proteins involved in ER-associated degradation (ERAD).

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Proteome and Ubiquitome Changes during Rose Petal Senescence

Project description:Petal senescence involves numerous programmed changes in biological and biochemical processes. Ubiquitination plays a critical role in protein degradation, a hallmark of organ senescence. Therefore, we investigated changes in the proteome and ubiquitome of senescing rose (Rosa hybrida) petals to better understand their involvement in petal senescence. Of 3859 proteins quantified in senescing petals, 1198 were up-regulated and 726 were down-regulated during senescence. We identified 2208 ubiquitinated sites including 384 with increased ubiquitination in 298 proteins and 1035 with decreased ubiquitination in 674 proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that proteins related to peptidases in proteolysis and autophagy pathways were enriched in the proteome, suggesting that protein degradation and autophagy play important roles in petal senescence. In addition, many transporter proteins accumulated in senescing petals, and several transport processes were enriched in the ubiquitome, indicating that transport of substances is associated with petal senescence and regulated by ubiquitination. Moreover, several components of the brassinosteroid (BR) biosynthesis and signaling pathways were significantly altered at the protein and ubiquitination levels, implying that BR plays important roles in petal senescence. Our data provide a comprehensive view of rose petal senescence at the posttranslational level.

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Ubiquitome profiling reveals metabolism related cell senescence and protein translation modified by UPL3

Project description:The HECT domain-containing UPL3 ligase plays critical roles in plant development and stress protection, but its mechanism of action remains unclear. To identify its targets in Arabidopsis thaliana, we conducted proteomic analyses of enriched ubiquitinated proteins in upl3 mutants via label-free mass spectrometry. In 6-week-old plants, a landscape of UPL3-dependent ubiquitinated proteins is constructed based on correlated datasets of ubiquitome, proteome, and transcriptome. Preferential ubiquitination of proteins related to carbon fixation and cell senescence represented the largest set of enriched ubiquitinated proteins that occurred in the upl3 plant, while a small set of reduced ubiquitinated proteins caused by the upl3 mutation were linked to cysteine/methionine synthesis and protein translational processes. Furthermore, the upl3 mutation led to an increase in ubiquitination of some of its targets including chromatin remodeling ATPase (BRM), histone proteins, and carbon metabolic enzymes, but decreased the ubiquitination of Hexokinase 1 (HXK1), Phosphoenolpyruvate carboxylase 2 (PPC2), ribosomal protein S5, and H1/H5 domain proteins. Notably, ubiquitin hydrolase 12 (UBP12), BRM, HXK1, and PPC2 were among the UPL3-interacting partners identified by both GFP-nanotrap-Mass-Spectroscopy analyses and yeast two-hybrid assay. Characterization of upl3, and brm-em, ubp12, ubp12ubp13 double mutant plants suggested that UPL3 fine-tuned carbon metabolism during cellular senescence by interacting, in the nucleus, with dually modified targets specific to histone variants, cell senescence, and the carbon metabolic pathway. Our results highlight an important function of UPL3 as a hub of regulated degradation.

2022-10-14 | PXD027037 | Pride

The Ubiquitin-modified Proteome of SARS-CoV-2-infected Host Cells Reveals Insights into Virus-Host Interaction and Pathogenesis

Project description:The outbreak of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed a serious threat to global public health. The mechanism of pathogenesis and host immune response to SARS-CoV-2 infection are largely unknown. In the present study, we applied a quantitative proteomic technology to identify and quantify the ubiquitination changes that occur in both the virus and Vero cells during SARS-CoV-2 infection. By applying label-free, quantitative LC-MS/MS proteomics, 8,943 lysine ubiquitination sites on 3,086 proteins were identified, of which 138 sites on 104 proteins were quantified as significantly upregulated, while 828 sites on 447 proteins were downregulated at 72 h post-infection. Bioinformatics analysis suggested that SARS-CoV-2 infection might modulate host immune responses through the ubiquitination of important proteins, including USP5, IQGAP1, TRIM28, and Hsp90. Ubiquitination modification was also observed on 11 SAR-CoV-2 proteins, including proteins involved in virus replication and inhibition of the host innate immune response. Our study provides new insights into the interaction between SARS-CoV-2 and the host as well as potential targets for the prevention and treatment of COVID-19.

2021-03-08 | PXD021097 | Pride

Proteomic analyses of lysine 2-hydroxyisobutyrylation in Fusarium graminearum in response to tebuconazole and carbendazim

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