PXD013215-2

PXD013215 is an original dataset announced via ProteomeXchange.

Title	APEX2-mediated proximity labeling of mitochondrial matrix and chromatin in budding yeast
Description	Enzyme-catalyzed proximity labeling (PL) with biotin is a novel approach to map organelle compartmentalization and protein interaction networks in living cells. Here, we present a new method based on semi-permeabilized yeast cells and the enzyme APEX2, an engineered ascorbate peroxidase. Combined with stable isotope labeling by amino acids in cell culture (SILAC), we demonstrate proteomic mapping of a membrane-enclosed and a semi-open compartment, the mitochondrial matrix and the nucleus. APEX2 PL revealed nuclear proteins that were previously not identified by conventional techniques. One of these, the Yer156C protein, is highly conserved but of unknown function. In follow-up experiments using quantitative PL with Yer156C-APEX2 we discovered an array of Yer156C interactors. Thus, our approach establishes APEX2 PL as an effective and versatile tool that complements the powerful methods palette for the model system yeast.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:03:03.908.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Nalpas
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-25 06:24:15	ID requested
1	2019-07-17 00:15:52	announced
⏵ 2	2024-10-22 04:03:04	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: budding yeast Yer156C interactome,Mitochondrial matrix, chromatin

Dr. Birgit Singer-Krüger
contact affiliation	Interfaculty Institute of Biochemistry Universität Tübingen Hoppe-Seyler-Straße 4 72076 Tübingen Germany
contact email	birgit.singer-krueger@uni-tuebingen.de
lab head
Nicolas Nalpas
contact affiliation	University of Rouen
contact email	nalpas.nicolas@gmail.com
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/2019/07/PXD013215

PRIDE project URI

• PRIDE
  1. PXD013215
     1. Label: PRIDE project
     2. Name: APEX2-mediated proximity labeling of mitochondrial matrix and chromatin in budding yeast