Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ubiquitinated proteins in Arabidopsis thaliana leaf tissue infected with Pseudomonas syringae

ABSTRACT: Ubiquitin signalling plays an indispensable role in plant immune signalling. Pathogen infection leads to rapid increases in the ubiquitinated proteome. Here, we identified ubiquitinated proteins and ubiquitination sites in Arabidopsis thaliana leaf tissue infected with the virulent pathogen Pseudomonas syringae pv. maculicola ES4326. Leaves of the Col-0 cultivar were pressure infiltrated with 2X107 cfu/ml of pathogen and samples harvested 24 hours post-inoculation.

INSTRUMENT(S):

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Cell Culture

SUBMITTER: Christos Spanos

LAB HEAD: Steven Spoel

PROVIDER: PXD074126 | Pride | 2026-02-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Wang_etal_2026_S8_UBQ_PSM.7z	Other
	Wang_etal_2026_S8_UBQ_PSM.raw	Raw
	checksum.txt	Txt

Items per page:

1 - 3 of 3

Similar Datasets

Mechanism of degrader-targeted protein ubiquitinability

Project description:Small molecule degraders of disease-driving proteins offer a clinically proven modality with enhanced therapeutic efficacy and the potential to tackle previously undrugged targets. Thermodynamically stable and kinetically long-lived degrader-mediated ternary complexes can drive faster, more profound and durable target degradation, however the mechanistic features by which they impact on target ubiquitination remain elusive. Here, we solve cryo-EM structures of the VHL Cullin 2 RING E3 ligase complexed with degrader MZ1, target protein Brd4BD2 and primed for catalysis with its cognate E2-ubiquitin bound. We find that Brd4BD2 adopts a favourable orientation towards the E2 active site. Mass spectrometry illuminates a patch of favourably ubiquitinable lysines on one face of in vitro ubiquitinated Brd4BD2, with Lys456 showing optimal distance and geometry for nucleophilic attack highlighted by cryo-EM. In vitro ubiquitination coupled with cellular degradation and ubiquitinomics confirm the importance of Lys456 and the ‘ubiquitination zone’ lysines. Our results demonstrate the proficiency of MZ1 in directing the substrate towards catalysis, explains the favourability of Brd4BD2 for ubiquitination bu UBE2R1, and reveals the flexibility of the enzyme in capturing sub-optimal lysines. We propose a model for ubiquitinability of degrader-recruited targets that provides a mechanistic blueprint for further rational drug design and optimization.

2024-11-08 | PXD053502 | Pride

Integrated phosphoproteomic profiling and causal analysis reveal signaling relations in GPVI/ITAM-mediated platelet activation programs

Project description:Platelets engage cues of pending endothelial dysfunction through coordinated adhesion, secretion and aggregation responses. These rapid changes in platelet phenotype are orchestrated by intracellular mechanisms that remain systematically undefined. This study develops a TMT-SPS-MS3 phosphoproteomics workflow to detail ~3,800 significant protein phosphorylation events associated with the progression of ITAM-mediated activation programs initiated by the platelet collagen receptor GPVI. With literature-guided causal inference tools, >200 site-specific signaling relations are mapped from phosphoproteomics data among key GPVI effectors (i.e., Syk, PLC gamma 2, PKC delta) and less characterized targets, including several Ras/MAPK axis proteins (i.e., KSR1). Networks highly regulated in GPVI/ITAM signaling out of context of curated knowledge are also highlighted, including Rab GTPase systems. In addition to serving as a model for generating and testing hypotheses from omics datasets, this study puts forth a means to identify hemostatic effectors and biomarkers relevant to thrombosis, vascular inflammation and other platelet-associated disease states.

2020-11-20 | PXD017167 | Pride

Modeling CRL4A ligase complex to predict target protein ubiquitination induced by CRBN-recruiting PROTACs

Project description:PROteolysis TArgeting Chimeras (PROTACs) are bifunctional small molecules that can simultaneously recruit target protein and E3 ligase to form a ternary complex (target protein / PROTAC / E3 ligase), leading to target protein ubiquitination and degradation via the Ubiquitin-Proteasome System (UPS). PROTACs have gained increasing attention in recent years due to certain advantages over traditional therapeutic modalities enabling targeting of previously "undruggable" proteins. To better understand the mechanism of PROTAC-induced Target Protein Degradation (TPD), several computational approaches have recently been developed to study and predict ternary complex formation. However, mounting evidence suggests that ubiquitination can also be a rate-limiting step in PROTAC induced TPD. Here, we propose a structure-based computational approach to predict target protein ubiquitination induced by CRBN-based PROTACs,

2022-05-19 | PXD030213 | Pride

Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B Cell Lymphoma

Project description:Polatuzumab Vedotin (Pola-V) is an antibody-drug conjugate directed to the CD79B subunit of the B cell receptor (BCR). When combined with conventional immunochemotherapy, Pola-V improves outcomes in DLBCL. To identify molecular determinants of sensitivity to Pola-V, we used CRISPR-Cas9 screening for genes that modulated the toxicity of Pola-V for lymphomas or the surface expression of its target, CD79B. Our results reveal a striking impact of CD79B glycosylation on Pola-V epitope availability on the lymphoma cell surface and on Pola-V toxicity. Genetic, pharmacological, and enzymatic approaches that remove terminal sialic acid residues from N-linked glycans enhanced lymphoma killing by Pola-V. Pola-V toxicity was also modulated by KLHL6, a ubiquitin ligase that targets CD79B for degradation in normal and malignant germinal center B cells, explaining its recurrent inactivation in germinal center-derived lymphomas. Our findings suggest precision medicine strategies to optimize Pola-V as a lymphoma therapeutic.

2024-07-12 | PXD043670 | Pride

: The Tip60 acetylome is a hallmark of the proliferative state in Drosophila

Project description:The acetyltransferase KAT5/Tip60 is a key epigenetic regulator of transcription and the DNA damage response. In Drosophila, Tip60 functions within the DOM-A complex to acetylate histones, but its broader substrate repertoire and cellular roles remain incompletely defined. Here, we comprehensively investigated the functions of Tip60 in a proliferative Drosophila cell model. Tip60 depletion caused cell cycle arrest, yet surviving cells exhibited resistance to mutagenic irradiation. This impaired proliferation was accompanied by reduced expression of critical cell cycle regulators, with Tip60 binding at their transcription start sites and Tip60-dependent acetylation of the histone variant H2A.V correlating with transcriptional activation. Beyond chromatin, Tip60 was found to acetylate a wide range of nuclear proteins involved in replication, mitosis, gene expression, chromatin organization, and ribosome biogenesis. These findings suggest that Tip60 coordinates the proliferative state through the combined regulation of histone and non-histone substrates. We propose that reversible acetylation of diverse effector proteins provides a mechanism for dynamically adjusting growth-related processes in response to cellular stress or nutrient availability. Collectively, this work identifies the DOM-A/Tip60 complex as a general promoter of cell proliferation.

2025-07-16 | PXD066107 | Pride

Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells

Project description:In this study, we analyzed the DNA methylation levels of 4799 IAP LTRs in three murine cell types: AB2.2 ES cells, somatic cells and a neuroblastoma cell line Neuro2A. According to the results, half of the IAP LTR retrotransposons show constant methylation patterns between the three cell types whereas the remaining half display variable levels of methylation. About half of the variably methylated IAP LTRs tend to be hypomethylated in ES cells, and nearly all of this group are hypomethylated in Neuro2A cells. Interestingly, the observed hypomethylation in both cell types occur in a non-uniform, locus-specific manner and to various degrees of severity, with some of them being easily detectible by COBRA. Overall, this study demonstrates the feasibility of HT-TREBS to study alterations in DNA methylation at retrotransposons in a locus-specific manner in multiple cell types and further suggests the potential utility of this technique in developing epigenetic biomarkers for tracking disease progression. HT-TREBS has been used with the Ion Torrent PGM platform to analyze the DNA methylation of 4799 IAP LTRs in a locus-specific manner in 3 cell types: somatic cells (previously submitted under GEO Accession GSE49222), AB2.2 ES cells and Neuro2A cells

2015-06-15 | E-GEOD-60007 | biostudies-arrayexpress

Circadian Proteomics Landscape of Mouse Livers Organized by Time-restricted Feeding: Ubiquitylation

Project description:Meal timing is essential in synchronization of circadian rhythms in different organ systems through clock-dependent and -independent mechanisms. The liver is a critical metabolic organ whose circadian clock and transcriptome can be readily reset by meal timing. However, it remains largely unexplored how circadian rhythms in the liver are organized in time-restricted feeding that intervenes meal timing. Here, we applied affinity-purification based shotgun proteomics for ubiquitylation to characterize circadian features associated with day/sleep- (DRF) and night/wake (NRF)-time restricted feeding in nocturnal female mice. The transcriptomics and metabolomics datasets are public (see www.circametdb.org.cn).

2023-08-22 | PXD038481 | Pride

Circadian Proteomics Landscape of Mouse Livers Organized by Time-restricted Feeding: Succinylation

Project description:Meal timing is essential in synchronization of circadian rhythms in different organ systems through clock-dependent and -independent mechanisms. The liver is a critical metabolic organ whose circadian clock and transcriptome can be readily reset by meal timing. However, it remains largely unexplored how circadian rhythms in the liver are organized in time-restricted feeding that intervenes meal timing. Here, we applied affinity-purification based shotgun proteomics for succinylation to characterize circadian features associated with day/sleep- (DRF) and night/wake (NRF)-time restricted feeding in nocturnal female mice. The transcriptomics and metabolomics datasets are public (see www.circametdb.org.cn).

2023-08-22 | PXD037604 | Pride

Large-scale identification of ubiquitination sites on membrane-associated proteins in Arabidopsis thaliana seedlings

Project description:Protein phosphorylation and ubiquitination are two of the most abundant forms of post-translational modifications in eukaryotes, regulated by thousands of protein kinases, phosphatases, E3 ubiquitin ligases, and ubiquitin proteases. Although previous studies have catalogued several ubiquitinated proteins in plants (Walton et al., 2016), few membrane-localized proteins have been identified. Receptor kinases (RKs) initiate phosphorylation signal relays that regulate plant growth, development, and stress responses. While the regulatory role of phosphorylation on protein kinase function is well-documented (Couto and Zipfel, 2016), considerably less is known about the role of ubiquitination on protein kinase function, even though protein turnover is critical to their signaling competence and cellular homeostasis. Here we describe the large-scale identification of ubiquitination sites on Arabidopsis proteins associated with or integral to the plasma membrane, including over 100 protein kinases.

2021-02-01 | PXD021992 | Pride

The Drosophila acetyltransferase chameau (chm) promotes starvation resilience at the expense of a shortened life span

Project description:Proteins involved in cellular metabolism and molecular regulation have been shown to extend lifespan in various laboratory organisms. However, for any improvement in aging to confer an evolutionary benefit, organisms must also be able to survive under non-ideal conditions. Earlier, we discovered that the loss of chm function and reduced activity resulted in several notable effects. Firstly, flies with a loss-of-function allele of chm exhibited an extended healthy lifespan when provided with an unrestricted food supply, indicating that chm plays a role in lifespan regulation. In this study, we demonstrate that these flies also experience a significant reduction in weight and decreased starvation resistance compared to flies with normal chm function. Furthermore, based on observations from transcriptomic, proteomic, and acetylome data, we hypothesize that chm is important for regulating metabolism in Drosophila, particularly in energy storage and utilization. Moreover, we demonstrate that reduced chm activity affects carbohydrate metabolism in flies at the basal level and during changes in nutrient status. In summary, this study suggests that chm is also required for starvation resilience by regulating carbohydrate metabolism, and the previously observed increase in survival time likely accompanies the inability to prepare for and cope with nutrient stress. Finally, as the ability to adapt and survive in a food-restricted environment was likely a stronger evolutionary driver than the ability to live a long life, chm is still present in the organism's genome despite its apparent deleterious effect on lifespan.

2023-09-05 | PXD042471 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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