PXD055137

PXD055137 is an original dataset announced via ProteomeXchange.

Title	Comparative proteome-wide abundance profiling of yeast strains deleted for Cdc48 adaptors
Description	The yeast ATPase Cdc48 (known as p97/VCP in human cells) plays an important role in the Ubiquitin Proteasome System. VCP is essential for cancer cell proliferation and its dysregulation has been implicated in several neurodegenerative diseases. Cdc48 functions by extracting ubiquitylated proteins from membranes, protein complexes and chromatin by often facilitating their proteasomal degradation. Specific adaptors or cofactors, primarily belonging to the UBX domain-containing protein family (which has seven members in S. cerevisiae), recruit Cdc48 to ubiquitylated proteins. Here, we employed sample multiplexing-based quantitative mass spectrometry to profile global protein abundance in p97 adaptors deleted strains, specifically comparing seven single deletion strains of UBX domain-containing proteins and the Cuz1 deletion strain which belongs to the zinc finger AN1-type domain protein family. We observed that each strain showed unique sets of differentially abundant proteins compared to wildtype. Our analysis also revealed a role for Ubx3 in maintaining wildtype levels of mitochondrial proteins. Overall, we identified ~1400 differentially abundant proteins in the absence of a specific Cdc48 adaptor. This unique dataset offers a valuable resource for studying the functions of these adaptors aiming to achieve a better understanding of the cellular processes regulated by Cdc48 itself and to deepen our understanding of the Ubiquitin Proteasome System.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_01:35:48.020.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; deaminated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-23 08:22:39	ID requested
⏵ 1	2025-05-07 01:35:48	announced

Rossio V, Paulo JA, Comparative Proteome-Wide Abundance Profiling of Yeast Strains Deleted for Cdc48 Adaptors. Proteomes, 12(4):(2024) [pubmed]

10.3390/proteomes12040031;

submitter keyword: Ubiquitin Proteasome System, S. cerevisiae, UBX domain-containing proteins,TMT proteomics, Cdc48, proteome

Joao A. Paulo
contact affiliation	Harvard Medical Schol Department of Cell Biology Boston, MA 02115 USA
contact email	joao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD055137
     1. Label: PRIDE project
     2. Name: Comparative proteome-wide abundance profiling of yeast strains deleted for Cdc48 adaptors