Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

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

Similar Datasets

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).

2020-03-20 | PXD005457 | Pride

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

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered post-translational modification in some prokaryotic and eukaryotic organisms. Here, we carried out proteome-wide analysis of Khib in Fusarium graminearum, identifying the reshaping of lysine 2-hydroxyisobutyrylome by tebuconazole or carbendazim, using the most recently-developed high-resolution LC-MS/MS in combination with high-specific affinity enrichment. In total, 3035 quantifiable Khib sites on 937 proteins were identified. With the criteria of fold changes over 1.3, normalized with total proteins, 1083 Khib sites of 509 proteins were considered as significantly affected by tebuconazole treatment, while 344 Khib sites of 227 proteins were significantly affacted by carbendazim. Furthermore, bioinformatics analysis were conducted.

2022-04-04 | PXD022499 | Pride

Proteome-wide analysis of Lysine 2-Hydroxyisobutyrylation in Candida albicans

Project description:Candida albicans is the most common human fungal pathogen, causing diseases ranging from mucosal to systemic infections for both immunocompetent and immunocompromised individuals. Lysine 2-hydroxyisobutyrylation is a highly conserved posttranslational modification found in a wide variety of organisms. In this study, we survey the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in C. albicans. Using an antibody-enrichment approach along with the traditional LC-MS/MS method, the pattern of Khib-modified proteins and sites were analyzed in one wild type strain of C. albicans. We identified 1438 Khib-modified proteins with 6659 modified sites in this strain, and a more detailed bioinformatics analysis indicated that the Khib-modified proteins are involved in a wide range of cellular functions with diverse subcellular locations. Functional enrichment analysis featured several prominent functional pathways, including ribosome, biosynthesis of antibiotics, biosynthesis of secondary metabolites, biosynthesis of amino acids and carbon metabolism – of which the ribosome pathway is the most affected pathway. Even when compared with the reported lysine acetylation (Kac) and succinylation (Ksuc), the Khib-modified sites on ribosomal proteins remained the highest for C. albicans. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and protein translation. Confirmation at the biochemical level would enable us to resolve physiological and pathogenic roles of PTM in C. albicans.

2021-01-15 | PXD023013 | Pride

Systematic Analysis of the Lysine Crotonylome and multiple PTM analysis (acetylation, succinylation and crotonylation) in Candida albicans

Project description:LC-MS/MS was used to carry out the analysis of the crotonylome in C. albicans (Candida albicans) comprehensively in our study. Generally, 5242 specific crotonylated sites of 1584 crotonylated proteins were detected among 9038 proteins in C. albicans. The crotonylome involved in the regulation of metabolism through the bioinformatics analysis. Moreover, the crotonylated proteins related to biosynthesis and carbon metabolism were prevalence phenomenon. Moreover, a universal rule were found in crotonylated motifs: D/E were found in the position (+1, +2 or +3) and K/R were found in the position (+5 or +6) of the residue; A/E/F/G/P/W/Y were found in the -1 position and A/K/R were found in the position (-5, -6, -7 or -8) of the residue. As far as we know, crotonylated histone sites that screened in C. albicans of this study have not been reported before. Furthermore, a variety of connections in PPI (protein-protein interaction network) of ribosome, oxidative phosphorylation, nucleus and proteasome were modified by acetylation, succinylation and crotonylation. Sir2 inhibitor AK-1 was able to promote histone lysine crotonylation and non-histone lysine crotonylation.

2021-01-08 | PXD018848 | Pride

Salt stress downregulates 2-hydroxybutyrylation in Arabidopsis siliques

Project description:In this study, we compared the siliques from Arabidopsis thaliana under salt stress (Ss) with those in the control (Cs). The results showed that Khib was abundant in siliques. However, there were certain significant differences between the Ss and the Cs: Totally 3,810 normalized Khib sites on 1,254 proteins were identified in siliques under salt stress, and Khib was up-regulated at 96 sites on 78 proteins while down-regulated at 282 sites on 205 proteins in Ss silique. Among them, 13 proteins, including F4IVN6, Q9M1P5, and Q9LF33, had sites with the most significant regulation Khib modification. Bioinformatics analysis suggests that Khib mainly participates in glycolysis/gluconeogenesis and endocytosis. In particular, there were 117 Khib-modified proteins that were mapped to the protein interaction database, and the proteins with the most significant up-regulation of Khib sites were on P46422, O82514, Q38970, Q9LD57, and Q9STW6, while the most down-regulated sites were on Q9M9K1, Q9SF16, O24456, P83484, Q9FWA3, and P54609. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism.

2021-12-30 | PXD028116 | Pride

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

2020-03-20 | PXD005470 | Pride

Salt-inhibited protein 2-hydroxyisobutyrylation affects silique development of Arabidopsis thaliana

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is one of the newly discovered post-translational modifications (PTMs) through protein acylation. It has been reported to be widely distribute in both eukaryotes and prokaryotes, and plays an important role in chromatin conformation change, gene transcription, subcellular localization, protein-protein interaction, signal transduction, and cellular proliferation. In this study, we compared the siliques from Arabidopsis thaliana under salt stress (Ss) with those in the control (Cs). The results showed that this highly conserved modification was abundant in siliques. However, there were certain significant differences between the Ss and the Cs: 3810 normalized 2-hydroxyisobutyrylation sites on 1254 proteins were identified in siliques under salt stress, and lysine 2-hydroxyisobutyrylation was up-regulated at 96 sites on 78 proteins while down-regulated at 282 sites on 205 proteins in Ss. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism. Overall, our work reveals the first systematic analysis of Khib proteome in Arabidopsis siliques under salt stress, and sheds a light on the future studies on the regulatory mechanisms of Khib during the salt stress response of plants.

2021-12-30 | PXD026643 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data