PXD016376

PXD016376 is an original dataset announced via ProteomeXchange.

Title	The Aspartic Protease Ddi1 Contributes to DNA-Protein Crosslink Repair in Yeast
Description	Naturally occurring and drug-induced DNA-protein crosslinks (DPCs) interfere with key DNA transactions if not timely repaired. The unique family of DPC-specific proteases Wss1/SPRTN targets DPC protein moieties for degradation, including topoisomerase-1 trapped in covalent crosslinks (Top1ccs). Here we describe that the efficient DPC disassembly requires Ddi1, another conserved predicted protease in Saccharomyces cerevisiae. We found Ddi1 in a genetic screen of the tdp1wss1 mutant defective in Top1cc processing. Ddi1 is recruited to a persistent Top1cc-like DPC lesion in an S-phase dependent manner to assist eviction of crosslinked protein from DNA. Loss of Ddi1 or its putative protease activity hypersensitize cells to DPC trapping agents independently from Wss1 and 26S proteasome, implying its broader role in DPC repair. Among potential Ddi1 targets we found the core component of RNAP II and show that its genotoxin-induced degradation is impaired in ddi1. Together, we propose that the Ddi1 protease contributes to DPC proteolysis. Yeast strains with WSS1 and DDI1 deletions were compared when either complemented with DDI1-WT or ddi1-D220A after hydroxyurea treatment by SILAC MS.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:00:30.108.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michael Plank
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-21 01:21:51	ID requested
1	2019-11-22 05:02:23	announced
2	2019-11-27 06:54:58	announced	2019-11-27: Updated project metadata.
⏵ 3	2024-10-22 05:00:30	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: LC-MSMS, crosslink repair,S.cerevisiae, SILAC, Ddi1

Robbie Loewith
contact affiliation	Department of Molecular Biology, Sc III, University of Geneva
contact email	Robbie.Loewith@unige.ch
lab head
Michael Plank
contact affiliation	University of Arizona
contact email	michael.plank@unige.ch
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/2019/11/PXD016376

PRIDE project URI

• PRIDE
  1. PXD016376
     1. Label: PRIDE project
     2. Name: The Aspartic Protease Ddi1 Contributes to DNA-Protein Crosslink Repair in Yeast