PXD043923

PXD043923 is an original dataset announced via ProteomeXchange.

Title	Quantitative mapping of autophagic cargo during nutrient stress reveals YIPF3 - YIPF4 as membrane receptors for Golgiphagy_part2_neurons
Description	During nutrient stress, macroautophagy is employed to degrade cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodeling the proteome. While the machinery responsible for initiation of macroautophagy is well characterized, our understanding of the extent to which individual proteins, protein complexes and organelles are selected for autophagic degradation, and the underlying targeting mechanisms is limited. Here, we use orthogonal proteomic strategies to provide a global molecular inventory of autophagic cargo during nutrient stress in mammalian cell lines. Through prioritization of autophagic cargo, we identify a heterodimeric pair of membrane-embedded proteins, YIPF3 and YIPF4, as receptors for Golgiphagy. During nutrient stress, YIPF4 is mobilized into ATG8-positive vesicles that traffic to lysosomes as measured via Golgiphagy flux reporters in a process that requires the VPS34 and ULK1-FIP200 arms of the autophagy system. Cells lacking YIPF3 or YIPF4 are selectively defective in elimination of Golgi membrane proteins during nutrient stress. By merging absolute protein abundance with autophagic turnover, we create a global protein census describing how autophagic degradation maps onto protein abundance and subcellular localization. Our results, available via an interactive web tool, reveal that autophagic turnover prioritizes membrane-bound organelles (principally Golgi and ER) for proteome remodeling during nutrient stress.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:03:04.675.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kelsey Hickey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetic acid derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-19 11:13:06	ID requested
1	2023-09-13 12:34:59	announced
⏵ 2	2024-10-22 06:03:05	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Human, autophagy, iNeurons

J. Wade Harper
contact affiliation	Department of Cell Biology, Harvard Medical School, Boston MA, USA
contact email	wade_harper@hms.harvard.edu
lab head
Kelsey Hickey
contact affiliation	HMS
contact email	kelsey_hickey@hms.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD043923
     1. Label: PRIDE project
     2. Name: Quantitative mapping of autophagic cargo during nutrient stress reveals YIPF3 - YIPF4 as membrane receptors for Golgiphagy_part2_neurons