PXD002648

PXD002648 is an original dataset announced via ProteomeXchange.

Title	De-novo synthesized targets of NMD and ER stress
Description	Nonsense-mediated mRNA decay (NMD) has originally been described as a surveillance mechanism to inhibit the expression of mRNAs with truncated open reading frames (ORFs) and to contribute to the fidelity of gene expression. It is now recognized that NMD also controls the expression of physiological genes with “intact” mRNA. Stress can decrease NMD efficiency and thus increase the mRNA levels of physiological NMD targets. As stress can also inhibit translation, the net outcome for shaping the proteome is difficult to predict. We have thus analyzed de-novo protein synthesis in response to NMD inhibition or the induction of mild endoplasmic reticulum (ER) stress by treatment of cells with the reducing agent dithiotreitol (DTT). We combined pulsed azidohomoalanine (AHA) and stable isotope labeling by amino acids in cell culture (SILAC). Labeled proteins were purified by click chemistry-based covalent coupling to agarose beads, trypsinized, fractionated, and analyzed by LC-MS/MS. We find that mild ER stress upregulates the de-novo synthesis of components of all three branches of the unfolded protein response (PERK, IRE1a and ATF6) without increasing eIF2a phosphorylation or impairing of protein translation. In contrast, inhibition of NMD induces de-novo protein synthesis of downstream targets of the PERK and IRE1a pathways but not the ATF6 pathway. These data thus support a model that implicates a positive feedback loop of ER stress inhibiting NMD efficiency which further promotes the ER stress response in a branch-specific manner.
HostingRepository	PRIDE
AnnounceDate	2016-02-22
AnnouncementXML	Submission_2016-02-22_00:31:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jana Sieber
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-08-03 00:49:48	ID requested
⏵ 1	2016-02-22 00:31:01	announced

Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE, Proteomic Analysis Reveals Branch-specific Regulation of the Unfolded Protein Response by Nonsense-mediated mRNA Decay. Mol Cell Proteomics, 15(5):1584-97(2016) [pubmed]

curator keyword: Technical

submitter keyword: AHA, click chemistry, pulsed SILAC, NMD, UPF1, UPR, DTT

Andreas E. Kulozik
contact affiliation	Department of Pediatric Oncology, Hematology, Immunology and Pulmonology University Medical Center for Children and Adolescents Im Neuenheimer Feld 430 D-69120 Heidelberg Germany ( lab head )
contact email	andreas.kulozik@med.uni-heidelberg.de
lab head
Jana Sieber
contact affiliation	Heidelberg University
contact email	j_loeber@gmx.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/02/PXD002648

PRIDE project URI

• PRIDE
  1. PXD002648
     1. Label: PRIDE project
     2. Name: De-novo synthesized targets of NMD and ER stress