Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of the ubiquitination landscape in Arabidopsis upl3 upl4 mutants

ABSTRACT: The ubiquitin-proteasome system (UPS) serves as the primary pathway regulating cellular homeostasis and environmental responses in eukaryotes. In this pathway, E3 ubiquitin ligases catalyse substrate ubiquitination, thereby marking targets for proteasomal degradation. UPL3 and UPL4 are proteasome-associated HECT-type ubiquitin ligases known to remodel substrate-attached ubiquitin chains at the proteasome, ensuring processive degradation. To investigate the role of UPL3/4 in regulating cellular ubiquitination, we enriched ubiquitinated proteins from wild-type and upl3 upl4 mutant seedlings using a Ubiquilin UBA domain tetramer. The purified ubiquitome was subsequently analysed by liquid chromatography-mass spectrometry (LC-MS).

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Cell Culture

SUBMITTER: Christos Spanos

LAB HEAD: Steven Spoel

PROVIDER: PXD072854 | Pride | 2026-08-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Wang_etal_2026_S1_WT_1.raw	Raw
	Wang_etal_2026_S2_WT_2.raw	Raw
	Wang_etal_2026_S3_WT_3.raw	Raw
	Wang_etal_2026_S7_upl3_upl4_1.raw	Raw
	Wang_etal_2026_S8_upl3_upl4_2.raw	Raw

Items per page:

1 - 5 of 8

Similar Datasets

The p53-dependent role of JAB1 in OS pathogenesis

Project description:JAB1 is a regulator of ubiquitin mediated protein degradation upstream of the 26S proteasome. JAB1 regulates the ubiquitin proteasome system through controlling the activity of the largest family of E3 ubiquitin ligases, the Cullin-RING Ligases. JAB1 is also a transcriptional co-factor contolling the expression of numerous genes and regulates musculoskeletal development in vivo. It is reported that JAB1 is overexpressed in many cancers, making it a potential oncogene. Thus, JAB1 has a highly spatiotemporal specific role in development and cancer pathogenesis. This study aims to determine the JAB1-mediated transcriptome that exists in osteosarcoma cells.

2020-06-10 | GSE117773 | GEO

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

Project description:TRIM25 is a novel RNA-binding protein and a member of the Tripartite Motif (TRIM) family of E3 ubiquitin ligases, which plays a pivotal role in the innate immune response. Almost nothing is known about its RNA-related roles in cell biology. Furthermore, its RNA-binding domain has not been characterized. Here, we reveal that RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain, which we postulate to be a novel RNA-binding domain. Using CLIP-seq and SILAC-based co-immunoprecipitation assays, we uncover TRIM25’s endogenous RNA targets and protein binding partners. Finally, we show that the RNAbinding activity of TRIM25 is important for its ubiquitin ligase function. These results reveal new insights into the molecular roles and characteristics of RNA-binding E3 ubiquitin ligases and demonstrate that RNA could be an essential factor for their biological functions.

2017-10-19 | PXD007960 | Pride

1-aminocyclopropane-1-carboxylic acid (ACC)-induced gene expression in wild-type Col-0, mutant upl3 upl4, mutant ein3-1, and mutant upl3 upl4 ein3-1 Arabidopsis thaliana plants

Project description:The plant hormone ethylene is involved in plant developmental, stress and environmental signalling. The ethylene signalling pathway is modulated by the master transcription factor EIN3. Here we examined the involvement of proteasome-associated UPL3 and UPL4 ubiquitin ligases in ethylene-responsive gene expression. We reveal that in absence of functional UPL3 and UPL4, plants show constitutive and enhanced activation or repression of ethylene-responsive genes in an EIN3-dependent manner. Ten-day old Arabidopsis thaliana seedlings of wild-type Col-0, mutant upl3 upl4, mutant ein3-1, and mutant upl3 upl4 ein3-1 were grown on MS media in an environmental chamber with 16/8 hour day/night light regime (120 mol m-2 s-1 light intensity) and 22 degrees Celsius. Seedlings were then transferred to 6-well plates and floated on the surface of water or 50 uM 1-aminocyclopropane-1-carboxylic acid (ACC). After 3 hours seedlings were harvested and for each treatment ~50 seedlings were pooled together into a single biological repeat. In total three independent biological repeats were collected. After harvesting seedlings were briefly dried on tissue and immediately frozen in liquid nitrogen until further analysis.

2021-10-05 | E-MTAB-10964 | biostudies-arrayexpress

ProteasomeID: quantitative mapping of proteasome interactomes and substrates for in vitro and in vivo studies

Project description:Proximity labeling coupled to mass spectrometry enables in situ mapping of protein-protein interactions. Here, we have developed a strategy based on tagging of proteasomes with promiscuous biotin ligases and a newly generated mouse model to monitor the interactome of proteasomes in vivo. We demonstrate that biotin ligases can be incorporated in fully assembled proteasomes without negative impact on proteasome activity. Analysis of proteins labeled by tagged proteasomes retrieved more than half of the known proteasome-interacting proteins in a single mass spectrometry analysis, including assembly factors, activators and ubiquitin-cycle related proteins. We optimized the protocol for processing of proximity labeled samples to minimize contamination from streptavidin and implemented Data Independent Acquisition (DIA) mass spectrometry for label-free analysis. We demonstrate the utility of our workflow by identifying novel proteasome-interacting proteins, charting interactomes across mouse organs, and showing that proximity-labeling can be used to identify both endogenous and small molecule-induced proteasome substrates.

2024-07-05 | PXD034874 | Pride

Ubiquitinated proteins in Arabidopsis thaliana leaf tissue infected with Pseudomonas syringae

Project description: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.

2026-02-12 | PXD074126 | Pride

Proteomic Profiling of Potential E6AP Substrates via Ubiquitin-based Photo-Crosslinking Assisted Affinity Enrichment

Project description:E6AP/UBE3A, the founding member of HECT-type (Homologous to E6AP C-terminus) E3 ligases, is implicated in human papillomaviruses (HPV)-mediated cervical cancer and neurodevelopmental disorders like Angelman and Dup15q syndromes. To elucidate the function of E3 ligases, knowledge about their substrates is crucial. Their identification, however, is challenging due to complex cross-reactivities between E2, E3 and their substrates. To address this, we developed a novel ubiquitin-based photo labeling approach for HECT-type ligases. Our method modifies ubiquitin with a diazirine moiety and attaches it to E6AP's active site using the ubiquitination cascade and a Cys to Lys mutation. The resulting E6AP-Ub conjugate enables substrate trapping via photoaffinity labeling and proteomic profiling. We validated this approach through literature comparison and identified Ub C-terminal hydrolase 7 (Uchl5/Uch37) as a new, proteasome-independent ubiquitination target of E6AP. This method expands the toolbox for substrate identification, potentially providing deeper insights into E6AP-related cellular processes and other HECT-type E3 ligases.

2025-01-27 | PXD055649 | Pride

Cockayne syndrome A and B proteins regulate the transcription arrest upon genotoxic stress through a ubiquitin/proteasome degradation process (ChIP-seq)

Project description:The rare genetic disease Cockayne syndrome (CS) results in mutations in CSA and CSB. Upon UV irradiation, RNA synthesis was arrested: RNA-seq showed 70% of down-regulated genes in common between CSA and CSB deficient cells. ATF3, the product of an immediate early gene was overexpressed and bound to its CRE/ATF site to inhibit its responsive genes. ChIP experiments showed that CSA/CUL4A/DDB1 together with CSB and MDM2, target ATF3. In vivo and in vitro experiments showed that ATF3 was ubiquitilated by a concerted action of CSA and MDM2 ubiquitin-ligases and was further eliminated by the proteasome concomitantly with the recruitment of RNA polymerase II to restart transcription. In CS cells, dysfunctional CSA or CSB were unable to assemble the ubiquitin/proteasome complex, thereby maintaining the ATF3-dependent transcription arrested. Though, in addition to their function in DNA repair, CSA and CSB might thus regulate the timing of DNA binding factors on its specific target site via the ubiquitin/proteasome machinery.

2017-12-01 | GSE87562 | GEO

Cockayne syndrome A and B proteins regulate the transcription arrest upon genotoxic stress through a ubiquitin/proteasome degradation process (RNA-seq)

2017-12-01 | GSE87540 | GEO

Transcriptional Regulation by Cullin Ubiquitin Ligases

Project description:Transcriptional Regulation by Cullin Ubiquitin Ligases

| PRJNA614537 | ENA

Antagonistic control of myofiber size and muscle protein quality control by the ubiquitin ligase UBR4 during aging

Project description:Sarcopenia is a degenerative condition that consists in the age-induced atrophy and functional decline of skeletal muscle cells (myofibers). A common hypothesis is that inducing myofiber hypertrophy should also reinstate myofiber contractile function but such model has not been extensively tested. Here, we find that the levels of the ubiquitin ligase UBR4 increase in skeletal muscle with aging, and that muscle-specific UBR4 loss rescues age-associated myofiber atrophy in mice. However, UBR4 promotes proteolysis by the proteasome and consequently UBR4 loss reduces the muscle specific force and accelerates the decline in muscle protein quality that occurs with aging in mice. Similarly, hypertrophic signaling induced via muscle-specific loss of UBR4 and of several other ubiquitin ligases consistently compromises muscle function and shortens lifespan in Drosophila by reducing protein quality control. Altogether, these findings indicate that ubiquitin ligases regulate in opposite fashion myofiber size and muscle protein quality control during aging.

2021-01-07 | GSE149637 | GEO

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