PXD022228

PXD022228 is an original dataset announced via ProteomeXchange.

Title	ULK1/2 DKO MEF phosphoproteomics
Description	Autophagy is a mechanism by which intracellular cargo are catabolised in the lysosome. It involves the formation of double membraned organelles termed autophagosomes, a complex process orchestrated by the serine/threonine kinase ULK complex and class III PI3 kinase VPS34. Unbiased screens for ULK substrates revealed that the phosphoproteome is significantly altered upon loss of Ulk1/2 and yielded a high confidence list of substrates, including VPS34 complex member VPS15 and AMPK complex member PRKAG2. We identified 6 new ULK substrate residues in the VPS15. Mutation of these VPS15 phosphoacceptors reduces autophagosome formation and autophagic flux in cells, and VPS34 activity in vitro. ULK phosphorylation of the major phosphosite in VPS15, serine 861, decreases both autophagy initiation and autophagic flux. Analysis of VPS15 knockout cells and the ULK substrate VPS34 serine 249 revealed two novel ULK-dependent phenotypes downstream of VPS15 removal: starvation-independent accumulation of ULK substrates and kinase activity-regulated recruitment of autophagy proteins to ubiquitin-positive structures, both of which occur upon VPS15 ablation and can be partially recapitulated by chronic VPS34 inhibition.
HostingRepository	PRIDE
AnnounceDate	2021-06-16
AnnouncementXML	Submission_2021-06-15_22:27:13.131.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Helen Flynn
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-28 08:12:53	ID requested
⏵ 1	2021-06-15 22:27:14	announced

Mercer TJ, Ohashi Y, Boeing S, Jefferies HBJ, De Tito S, Flynn H, Tremel S, Zhang W, Wirth M, Frith D, Snijders AP, Williams RL, Tooze SA, Phosphoproteomic identification of ULK substrates reveals VPS15-dependent ULK/VPS34 interplay in the regulation of autophagy. EMBO J, 40(14):e105985(2021) [pubmed]

submitter keyword: Autophagy, autophagosome, ULK1, ULK2, VPS15, p150, PIK3R4, PRKAG2, VPS34, PI3 kinase, LC-MS/MS, SILAC, Phosphoproteomics, Orbitrap ULK1, ULK2, Mouse embryonic fibroblasts, amino acid starvation, SILAC, TMT

Bram Snijders
contact affiliation	Mass Spectrometry Proteomics The Francis Crick Institute Midland Road London NW1 1AT UK
contact email	bram.snijders@crick.ac.uk
lab head
Helen Flynn
contact affiliation	The Francis Crick Institute
contact email	helen.flynn@crick.ac.uk
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/2021/06/PXD022228

PRIDE project URI

• PRIDE
  1. PXD022228
     1. Label: PRIDE project
     2. Name: ULK1/2 DKO MEF phosphoproteomics