Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Substrates identification of yeast Ubp2 through DILUS

ABSTRACT: SILAC-based substrates identification of yeast Ubp2

ORGANISM(S): Saccharomyces Cerevisiae

SUBMITTER: Xu Ping

PROVIDER: PXD017357 | iProX | Mon Feb 03 00:00:00 GMT 2020

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

Ubiquitin Linkage Specificity of Deubiquitinases Determines Cyclophilin Nuclear Localization and Degradation.

Li Yanchang Y Lan Qiuyan Q Gao Yuan Y Xu Cong C Xu Zhongwei Z Wang Yihao Y Chang Lei L Wu Junzhu J Deng Zixin Z He Fuchu F Finley Daniel D Xu Ping P

iScience 20200313 4

Ubiquitin chain specificity has been described for some deubiquitinases (DUBs) but lacks a comprehensive profiling in vivo. We used quantitative proteomics to compare the seven lysine-linked ubiquitin chains between wild-type yeast and its 20 DUB-deletion strains, which may reflect the linkage specificity of DUBs in vivo. Utilizing the specificity and ubiquitination heterogeneity, we developed a method termed DUB-mediated identification of linkage-specific ubiquitinated substrates (DILUS) to scr ...[more]

PMID: 32240951

Similar Datasets

Genome-wilde identification of decapping substrates in the yeast Saccharomyces cervisiae

Project description:Genome-wilde identification of decapping substrates in the yeast Saccharomyces cervisiae

| PRJNA421669 | ENA

SILAC quantificaiton of yeast DUB UBP7

Project description:SILAC quantificaiton of yeast DUB UBP7's substrates

| PXD041289 |

A High Resolution Profile of NMD Substrates in Yeast

Project description:We report a high resolution catalouge of NMD substrates using RNA-Seq. We discovered several hundred new substrates for NMD. Using published ribosome footprint profiling data, we measured ribosome densities of normal-looking NMD substrates and non-NMD substrates. NMD substrates exhibited a striking difference in normalized ribosome occupancy in wild-type and UPF1 cells. We also found that normal looking NMD substrates have higher ratio of out of frame reads, lower codon optimalites and a higher propensity to have long stretches of non-optimal codons.

2016-12-02 | GSE86428 | GEO

O-GlcNAc transferase recognizes protein substrates using an asparagine ladder in the TPR superhelix

Project description:Abstract: The essential mammalian enzyme O-GlcNAc Transferase (OGT) is uniquely responsible for transferring N-acetylglucosamine to over a thousand nuclear and cytoplasmic proteins, yet there is no known consensus sequence and it remains unclear how OGT recognizes its substrates. To address this question, we have developed a protein microarray assay that chemoenzymatically labels de novo sites of glycosylation with biotin, allowing us to simultaneously as-sess OGT activity across >6000 human proteins. We used this assay to examine the contribution of a conserved asparagine ladder within the lumen of OGT’s superhelical tetratri-copeptide repeat (TPR) domain to substrate selection. When these residues were mutated, OGT retained full activity against short peptides, but showed low to no activity against most of the OGT substrates on the microarray. O-GlcNAcylation of protein substrates in cell extracts was also greatly attenuated. We conclude that OGT recognizes a majority of its substrates by binding them to the asparagine ladder in the TPR lumen proximal to the catalytic domain. This series contains microarray data both comparing the new chemoenzymatic method to antibody-based detection as well as comparing arrays treated with wild-type OGT, 5N5A mutant OGT, or controls not treated with enzyme. Note: all CTD-stained arrays or control array raw files are contained in GSE107911_RAW.tar

2018-02-26 | GSE107911 | GEO

Fruquintinib DDI Study With P-gp and BCRP Substrates

Project description:Fruquintinib DDI Study with P-gp and BCRP Substrates

| 2729773 | ecrin-mdr-crc

Genome-wilde identification of decapping substrates in the yeast Saccharomyces cervisiae

Project description:To assess the roles of the Dcp2 C-terminal domain and the decapping activators Pat1, Lsm1, and Dhh1 in mRNA decapping, we used RNA-Seq to analyze the expression profiles of yeast cells harboring a truncation of the Dcp2 C-terminal domain, mutations that render Dcp2 catalytically inactive, or deletions of the PAT1, LSM1, and DHH1 genes. Consistent with our recent model for decapping regulation, we found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation and that loss of these control functions causes significant deregulation of mRNA decapping; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap and, as expected, are targeted to decapping-dependent decay.

2017-12-09 | GSE107841 | GEO

pSILAC mass spectrometry reveals ZFP91 as novel IMiD dependent substrate of the CRL4CRBN ligase

Project description:Thalidomide and its derivatives lenalidomide and pomalidomide (IMiDs) are effective treatments of hematologic malignancies. It was shown that IMiDs impart gain of function properties to the CUL4-RBX1-DDB1-CRBN (CRL4CRBN) ubiquitin ligase that enable binding, ubiquitination and degradation of key therapeutic targets such as IKFZ1, IKZF3 and CSNK1A1. While these substrates have been implicated as efficacy targets in multiple myeloma (MM) and 5q deletion associated myelodysplastic syndrome (del(5q)-MDS), other targets likely exist. Using a pulse-chase SILAC mass spectrometry-based proteomics approach, we demonstrate that lenalidomide induces the ubiquitination and degradation of ZFP91. We establish that ZFP91 is a bona fide IMiD dependent CRL4CRBN substrate and further show that ZFP91 harbors a zinc finger (ZnF) motif, related to the IKZF1/3 ZnF, critical for IMiD dependent CRBN binding. These findings demonstrate that single time point pulse-chase SILAC mass spectrometry-based proteomics (pSILAC-MS) is a sensitive approach for target identification of small molecules inducing selective protein degradation.

2017-03-01 | GSE94728 | GEO

Yeast ubiquitin ligase LC-MS/MS

Project description:Ubiquitin ligases (E3s) serves as a key regulator for ubiquitylation-mediated pathway. The identification of the corresponding relationship between E3 and its substrates is challenging but required for understanding the regulatory network of ubiquitylation. The low abundance of ubiquitinated conjugates and high redundancy of E3s-substrates regulation made screening pretty hard. Herein, we combined SILAC-based quantitative proteomics with two contrary genetic methods (overexpression and knockout) in theory for E3 (Hrt3, F-box subunit of SCF complex) substrates screening.

2019-12-06 | PXD015654 | Pride

Identification of protein substrates of the Cullin-RING E3 ubiquitin ligase CRL4 through its substrate recognition factors DCAFs

Project description:Cullin-RING finger Ligases (CRLs) represent the largest family of E3 ubiquitin ligases and are responsible for ubiquitination of ~20% of cellular proteins degraded through the proteasome, catalyzing the transfer of E2-loaded ubiquitin to a substrate. Eight Cullins were described in vertebrates and among them, CUL4 associates with DDB1 acting as an adaptor to form the CUL4-DDB1 ubiquitin ligase complex, involved in protein ubiquitination and regulation of many cellular processes. The specificity of CUL4-DDB1 is mediated by substrate recognition adaptors named DDB1/CUL4 associated factors (DCAFs), which are characterized by the presence of a short structural motif of approximately 40 amino acids terminating in a tryptophan (W)-aspartic acid (D) dipeptide, the WD40 domain. Using different approaches (bioinformatics/structural analyses), independent studies suggested at least 60 different WD40 containing proteins that could act as adaptors for the DDB1/CUL4 complex. In this study, we aimed to validate the DCAFs based on their interaction with DDB1 and to define new partners and potential substrates of each DCAF using affinity purification followed by mass spectrometry. Using BioID and AP-MS approaches, we confirmed seven WDR40 protein that can be considered as DCAF with a high confidence level. Because identification of protein substrates of E3-ubiquitin ligases is not always guaranteed by identifying protein interactions, changes in protein stability and protein degradation was measured by pulse-SILAC to identify the protein substrates targeted for proteasomal degradation by each DCAFs. In conclusion, this work provides new insights into the roles of DCAFs as substrate adaptors for the DDB1-CUL4 complex, identifies the proteins targeting and the cellular processes that are involved.

2023-10-24 | PXD037482 | Pride

QUILT-2.025 NANT Neoepitope Yeast Vaccine (YE-NEO-001): Adjuvant Immunotherapy Using a Personalized Neoepitope Yeast-Based Vaccine To Induce T-Cell Responses In Subjects W/ Previously Treated Cancers.

Project description:This is a phase 1 study to evaluate the safety, the Recommended Phase 2 Dose (RP2D), and preliminary efficacy of a personalized neoepitope yeast-based vaccine, YE-NEO-001, in subjects who have completed potentially curative therapy for their solid cancer and who would otherwise be entering a period of surveillance for recurrent disease.

| 2275044 | ecrin-mdr-crc

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