PXD007159

PXD007159 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomics of affinity purified yeast NMD complexes
Description	Nonsense-mediated mRNA decay (NMD) is a major translation-dependent RNA degradation pathway required for embryo development and telomere maintenance. Core NMD factors Upf1, Upf2 and Upf3 are conserved from yeast to mammals but a model of the NMD machinery compatible with all eukaryotes is not yet available. We performed the first large-scale quantitative characterization of yeast NMD complexes through affinity purification and mass-spectrometry with 7 different NMD-related factors, with or without Rnase, in strains deleted or not for NMD genes. This extensive characterization of NMD complexes identified two distinct complexes associated with Upf1: Detector (Upf1/2/3) and Effector. Effector contained, in addition to Upf1, the mRNA decapping enzyme and two potential equivalents of mammalian Smg6/5/7: Nmd4 and Ebs1. Like the Smg proteins, Nmd4 and Ebs1 were required for efficient NMD. Our results suggest that the core eukaryotic NMD machinery is conserved across species and operates through successive Upf1-bound Detector and Effector complexes.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:49:39.025.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cosmin Saveanu
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-31 06:54:57	ID requested
1	2018-03-12 05:47:45	announced
2	2018-03-14 01:30:22	announced	Updated project metadata.
3	2018-05-23 02:01:25	announced	Updated project metadata.
⏵ 4	2023-11-14 08:49:39	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: LTQ-Orbitrap Velos,LC-MS/MS, affinity purification, yeast, MaxQuant, label-free, TAP

Alain Jacquier
contact affiliation	Genetics of Macromolecular Interactions Genomes and Genetics Department 25-28 rue du docteur Roux 75015 Paris, FRANCE
contact email	alain.jacquier@pasteur.fr
lab head
Cosmin Saveanu
contact affiliation	Institut Pasteur, Paris, France
contact email	cosmin.saveanu@pasteur.fr
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/2018/03/PXD007159

PRIDE project URI

• PRIDE
  1. PXD007159
     1. Label: PRIDE project
     2. Name: Quantitative proteomics of affinity purified yeast NMD complexes