Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Yeast N-terminome SILAC - Formyl-methionine as an N-degron of a eukaryotic N-end rule pathway

ABSTRACT: Discerning yeast N-termionome with SILAC method. To analyze qualitative and quantitative analysis of N-formyl-methionine when introducing environmental stress.

INSTRUMENT(S): Q Exactive

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

SUBMITTER: Shinyeong Ju

LAB HEAD: Cheolju Lee

PROVIDER: PXD010780 | Pride | 2019-11-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Formyl-methionine as an N-degron of a eukaryotic N-end rule pathway.

Kim Jeong-Mok JM Seok Ok-Hee OH Ju Shinyeong S Heo Ji-Eun JE Yeom Jeonghun J Kim Da-Som DS Yoo Joo-Yeon JY Varshavsky Alexander A Lee Cheolju C Hwang Cheol-Sang CS

Science (New York, N.Y.) 20181108 6418

In bacteria, nascent proteins bear the pretranslationally generated N-terminal (Nt) formyl-methionine (fMet) residue. Nt-fMet of bacterial proteins is a degradation signal, termed fMet/N-degron. By contrast, proteins synthesized by cytosolic ribosomes of eukaryotes were presumed to bear unformylated Nt-Met. Here we found that the yeast formyltransferase Fmt1, although imported into mitochondria, could also produce Nt-formylated proteins in the cytosol. Nt-formylated proteins were strongly up-reg ...[more]

PMID: 30409808

Similar Datasets

Formyl-methionine as an N-degron of a eukaryotic N-end rule pathway.

Project description: Not available

| S-EPMC6551516 | biostudies-literature

N-terminome profiling in HEK293T

Project description:Various forms of the protein, called proteoform, are generated by co- or post-translational modification, alternative splicing and alternative translation initiation site, resulting in interactions between ribosomes, mRNAs, tRNAs, and various enzymes. Here, we introduce a N-terminal peptide enrichment method (Nrich) using a negative selection on filter for the N-terminal peptides with two chemical reagents for labeling free amine and two endoproteases. We identified 6,525 acetylated (or partially acetylated) and 6,570 free protein N-termini from 5,727 proteins. The protein N-termini can be classified into nine groups, such as initial methionine removed or retained, non-terminal residue, signal/transit/pro-peptide removal, putative alternative translational initiation site (methionine removed or retained) and unknown processing, suggesting various proteoform in vivo. In addition, novel protein N-termini was identified in 5`-UTR sequence with pseudo start codon using customized database. Nrich can obtain information about protein stability, localization and function through the observation of finished N-terminal sequence of mature protein.

2017-08-17 | PXD005583 | Pride

The Functional Human C-Terminome.

Project description: Not available

| S-EPMC4822787 | biostudies-literature

Quantitative N-terminome of N-end rule mutant in Arabidopsis

Project description:According to the /N-end rule pathway, proteins with basic N-termini are targeted for degradation by the Arabidopsis thaliana E3 ligase, PROTEOLYSIS6 (PRT6). Here, we undertook a quantitative proteomics study of N-end rule mutant prt6, to investigate the impact of this pathway on the etiolated seedling. Isolation of N-terminal peptides using terminal amine isotope labelling of samples (TAILS) combined with Tandem mass tag (TMT) identified over 3000 unique N-termini. Trypsin and GluC have advantage of identification of Acetylated or neo-peptides respectively. Seed storage proteins and Cysteine proteins actives are differentially regulated in abundance in the prt6 mutants, which are represent downstream targets of transcription factors known to be N-end rule substrates.

2017-10-27 | PXD006450 | Pride

Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits.

Project description: Not available

| S-EPMC3680069 | biostudies-literature

AAPs rule!

Project description:Aerobic anoxygenic phototrophs: their role in carbon utilization under light in freshwater ecosystems

| PRJEB41596 | ENA

N-degron and C-degron pathways of protein degradation.

Project description: Not available

| S-EPMC6329975 | biostudies-literature

The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner

Project description:Chromatin insulators are DNA-protein complexes situated throughout the genome that contribute to higher order organization and demarcation into distinct transcriptional domains. Mounting evidence in different species implicates RNA and RNA-binding proteins as regulators of chromatin insulator activities. Here we identify the Drosophila hnRNP M homolog Rumpelstiltskin (Rump) as an antagonist of gypsy chromatin insulator enhancer-blocking and barrier activities. Despite ubiquitous expression of Rump, improvement of barrier activity is detected only in tissue outside of the central nervous system (CNS) when Rump levels are reduced. Furthermore, rump mutants restore insulator complex localization in an otherwise compromised genetic background only in non-CNS tissues. Rump associates physically with core gypsy insulator proteins, and ChIP-Seq analysis of Rump demonstrates extensive colocalization with a subset of gypsy insulator sites across the genome. The genome-wide binding profile and tissue-specificity of Rump contrast with that of Shep, a recently identified RNA-binding protein that antagonizes gypsy insulator activity exclusively in the CNS. Our findings indicate parallel roles for RNA-binding proteins in mediating tissue-specific regulation of chromatin insulator activity. ChIP-seq of Rump, Mod(mdg4)2.2, Shep, Su(Hw), and CP190 in Drosophila Kc167 cells

2014-04-18 | E-GEOD-51462 | biostudies-arrayexpress

Aminoacyl-transferases and the N-end rule pathway of prokaryotic/eukaryotic specificity in a human pathogen.

Project description: Not available

| S-EPMC1413915 | biostudies-literature

TRiC controls transcription resumption after UV damage by regulating Cockayne Syndrome protein A

Project description:Transcription-blocking DNA lesions are removed by transcription-coupled nucleotide excision repair (TC-NER) to preserve cell viability. TC-NER is triggered by the stalling of RNA polymerase II at DNA lesions, leading to the recruitment of TC-NER-specific factors such as the CSA-DDB1-CUL4A-RBX1 cullin-RING ubiquitin ligase complex (CRLCSA). Despite its vital role in TC-NER, little is known about the regulation of the CRLCSA complex during TC-NER. Using conventional and cross-linking immunoprecipitations coupled to mass spectrometry, we uncover a stable interaction between CSA and the TRiC chaperonin. TRiC’s binding to CSA ensures its stability and DDB1-dependent assembly into the CRLCSA complex. Consequently, loss of TRiC leads to mislocalization and depletion of CSA, as well as impaired transcription recovery following UV damage, suggesting defects in TC-NER. Furthermore, Cockayne syndrome (CS)-causing mutations in CSA lead to increased TRiC binding and a failure to compose the CRLCSA complex. Thus, we uncover CSA as a novel TRiC substrate and reveal a role for TRiC in regulating CSA-dependent TC-NER and the development of CS.

2018-05-02 | PXD008868 | 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