Browse
Submit Data
Databases
API
Help

Dataset Information

282 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of the ubiquitinated peptides using the yeast Rpt2-normal, G2A and G2delta strains

ABSTRACT: Ubiquitinated peptides (KGG peptides) purified from the yeast strains with or without mutation on the N-myristoylation site of the proteasome Rpt2 subunit were analyzed by an LTQ-Orbitrap Velos. The MS data was analyzed by the Progenesis LC-MS software.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Ayuko Kimura

LAB HEAD: Hisashi Hirano

PROVIDER: PXD002274 | Pride | 2017-08-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

N-Myristoylation of the Rpt2 subunit of the yeast 26S proteasome is implicated in the subcellular compartment-specific protein quality control system.

Kimura Ayuko A Kurata Yoichi Y Nakabayashi Jun J Kagawa Hiroyuki H Hirano Hisashi H

Journal of proteomics 20150904

Ubiquitination is the posttranslational modification of a protein by covalent attachment of ubiquitin. Controlled proteolysis via the ubiquitin-proteasome system (\UPS) alleviates cellular stress by clearing misfolded proteins. In budding yeast, UPS within the nucleus degrades the nuclear proteins as well as proteins imported from the cytoplasm. While the predominantly nuclear localization of the yeast proteasome is maintained by the importin-mediated transport, N-myristoylation of the proteasom ...[more]

PMID: 26344132

Similar Datasets

Changes to SUMO-modified proteome and total cellular proteome during EBV ractivation in AGS gastric carcinoma cells

Project description:To monitor changes to cellular and viral SUMO-modified proteins during EBV reactivation. SUMO1 and SUMO2 conjugates were studied using KGG mutant forms of SUMO and GG-K specific antibody enrichment of SUMO modified peptides. Time-points of 12h and 24h post-reactivation were monitored. Total cellular proteome was also analysed to study changes to the total protein levels of proteins under the same conditions.

2023-06-19 | PXD034631 | Pride

Identification of SUMO targets required to maintain human stem cells in the pluripotent state. - Characterisation of 6His-SUMO-KGG-mCherry ChiPS4 cells

Project description:To determine the role of SUMO modification in the maintenance of pluripotent stem cells we used ML792, a potent and selective inhibitor of SUMO Activating Enzyme. Treatment of human induced pluripotent stem cells with ML792 initiated changes associated with loss of pluripotency such as reduced expression of key pluripotency markers. To identify putative effector proteins and establish sites of SUMO modification, cells were engineered to stably express either SUMO1 or SUMO2 with TGG to KGG mutations that facilitate GlyGly-K peptide immunoprecipitation and identification. A total of 976 SUMO sites were identified in 427 proteins. STRING enrichment created 3 networks of proteins with functions in regulation of gene expression, ribosome biogenesis and RNA splicing, although the latter two categories represented only 5% of the total GGK peptide intensity. The remainder have roles in transcription and chromatin structure regulation. Many of the most heavily SUMOylated proteins form a network of zinc-finger transcription factors centred on TRIM28 and associated with silencing of retroviral elements. At the level of whole proteins there was only limited evidence for SUMO paralogue-specific modification, although at the site level there appears to be a preference for SUMO2 modification over SUMO1 in acidic domains. We show that SUMO is involved in the maintenance of the pluripotent state in hiPSCs and identify many chromatin-associated proteins as bona fide SUMO substrates in human induced pluripotent stem cells.

2021-11-03 | PXD023241 | Pride

Identification of SUMO targets required to maintain human stem cells in the pluripotent state. - Identification of SUMO modified proteins from hiPS cells

2021-11-03 | PXD028050 | Pride

Ubiquitinated proteome of E15.5 murine cortical neurons

Project description:TRIM9 and TRIM67 are neuronally-enriched E3 ubiquitin ligases essential for neuronal morphogenesis and responses to the axon guidance cue netrin-1. Deletion of either gene in the mouse results in subtle neuroanatomical anomalies yet overt deficits in spatial learning and memory. The identify of few TRIM9 or TRIM67 substrates are known. Here we performed ubiquitin remnant profiling approach (Xu et al., 2010)in cultured cortical neurons from murine wildtype, Trim9-/-, Trim67-/-, and Trim9-/-:Trim67-/- embryos cultured with or without netrin-1 supplementation to attempt to identify proteins with altered ubiquitination. Although batch variability hindered our ability to identify differential protein ubiquitination, the results delineate the neuronal ubiquitionome during neurite outgrowth, axon specification, and axon branching.

2021-01-04 | PXD021818 | Pride

Quantification of poly-ubiquitinated proteins in wild type Arabidopsis and amiNAA10 plants

Project description:Wild type Arabidopsis Col-0 plants and mutants depleted of the catalytic subunit of the ribosome-associated N-acetyltransferase A (NatA) complex (amiNAA10) were grown on soil for six weeks under short-day conditions (8h light, light intensity: 100 µE, 21 °C/18 °C temperature (day/night), 50 % humidity). Proteasome and deubiquitinase activity were inhibited at 10 am (2 h of light) by floating leaf discs on ½ Hoagland supplemented with 50 µM MG132 and 20 µM PR-619 for 5 h.

2022-04-04 | PXD024329 | Pride

Identification of ubiquitinated proteins in lung adenocarcinoma and normal lung tissues

Project description:To identify ubiquitinated modified proteins of lung adenocarcinoma, we collected five pairs of lung adenocarcinoma and normal lung tissues from the clinic for analysis

2022-01-12 | PXD027001 | Pride

Recognition of ubiquitinated nucleosomes.

Project description: Not available

| S-EPMC5373988 | biostudies-literature

Inhibition of protein N-myristoylation blocks Plasmodium falciparum intracellular development and egress, but myristoylation of GAP45 is required only for erythrocyte invasion.

Project description:Inhibition of protein N-myristoylation blocks Plasmodium falciparum intracellular development and egress, but myristoylation of GAP45 is required only for erythrocyte invasion. TMT quantification used to determine protein expression changes upon inhibition of myristoylation

2021-10-07 | PXD021879 | Pride

Lipid-anchored Proteasomes Control Membrane Protein Homeostasis

Project description:As the major protein degradation machinery of eukaryotic cells, the 26S proteasome is generally thought to localize in the nucleus and cytosol. A portion of proteasomes are known to associate with various membrane structures of the cell, the mechanism and biological meaning of which have been elusive. Here we show that N-myristoylation of the proteasome subunit Rpt2 is an evolutionarily conserved determinant of proteasome-membrane interaction. Loss of this modification leads to embryonic lethality in mice, significant reduction of migration ability in MEFs and profound changes in the membrane-associated proteome as determined by SILAC-MS, suggesting a key role of membrane-tethered proteasomes in carrying out compartmentalized protein degradation. And the tumorigenicity is reduced in the oncogene-transformed MEF without modification. Serendipitously, we found that the Rpt2-G2A mutation cell lines confers partial resistance to proteasome inhibitors, such as Bortezomib and MG132. Thus, N-myristoylation of Rpt2 determines the localization and activity of the proteasome at the membrane, which is critical for embryogenesis, cellular homeostasis and tumorigenesis.

2023-05-16 | GSE232308 | GEO

Ubiquitinated PCNA drives USP1 synthetic lethality in cancer

Project description:CRISPR Cas9-based functional genomics screening is a powerful approach for identifying and characterizing novel oncology drug targets. Here, we elucidate the synthetic lethal mechanism of deubiquitinating enzyme USP1 in cancers with underlying DNA damage vulnerabilities, specifically BRCA1/2 mutant tumors and a subset of BRCA1/2 wild-type (WT) tumors. In sensitive cells, pharmacological inhibition of USP1 leads to decreased DNA synthesis concomitant with the induction of S-phase-specific DNA damage. Genome-wide CRISPR-Cas9 screens identified RAD18 and UBE2K, which promote PCNA mono- and polyubiquitination respectively, as downstream mediators of USP1 dependency. The accumulation of mono- and polyubiquitinated PCNA following USP1 inhibition was associated with a reduction in total PCNA protein levels. Ectopic expression of WT and ubiquitin-dead K164R PCNA reversed USP1 inhibitor sensitivity. Our results demonstrate, for the first time, that USP1 dependency hinges on the aberrant processing of mono- and polyubiquitinated PCNA. Moreover, this mechanism of USP1 dependency extends beyond BRCA1/2 mutant tumors to a novel subset of BRCA1/2 WT cancer enriched in ovarian and lung lineages. We further show PARP and USP1 inhibition are strongly synergistic in BRCA1/2 mutant cell lines and xenograft models. We postulate USP1 dependency unveils a previously uncharacterized vulnerability linked to post-translational modifications of PCNA. Taken together, USP1 inhibition may represent a unique therapeutic strategy for BRCA1/2 mutant tumors and a subset of BRCA1/2 WT tumors.

2022-09-27 | GSE214121 | GEO

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