PXD032378

PXD032378 is an original dataset announced via ProteomeXchange.

Title	A palmitoyl transferase chemical genetic system to map ZDHHC-specific S-acylation
Description	ZDHHC S-acyltransferases catalyze the transfer of fatty acyl groups, primarily palmitate, to cysteine residues of substrate proteins in all eukaryotes. The 23 human ZDHHCs are known to S-acylate an extensive network of proteins essential to normal physiology, including many which are dysregulated in disease. Current technologies for whole proteome analyses of S-acylation do not directly associate a specific ZDHHC with its substrates, making it difficult to link a ZDHHC to specific mechanisms or disease phenotypes. Here, we present a solution to this challenge through development and validation of the first ZDHHC chemical genetic systems. Intact cells expressing a ZDHHC engineered to carry a ‘hole’ mutation in the lipid binding domain were metabolically labeled with a synthetic, chemically-tagged fatty acid probe carrying a matching ‘bump’, resulting in selective fatty acid probe transfer to substrates of the mutant ZDHHC. ZDHHC/probe pairs were exemplified for efficient and selective transfer to ZDHHCs 3, 7, 11, 15 and 20, and adapted to chemical proteomic analysis for ZDHHCs 7, 15 and 20, generating the first de novo substrate profiles for these ZDHHC isozymes across three different cell lines. These data reveal extensive ZDHHC-specific substrate sets across more than 300 total identified substrates, in addition to substrates common between cell lines and between ZDHHCs, and several functionally diverse ZDHHC20 substrates were validated in targeted assays and the sites of S-acylation determined. The chemical genetic platform described here offers a novel and versatile approach to explore ZDHHC substrates and S-acylation biology, with the potential to encompass ZDHHCs across a wide range of eukaryotic organisms. This submission contains data relating to the determination of changes in S-acylated proteins using YnPal and DHHC20 CRISPR Cas9 KO cells, alongside determining the interactome of ZDHHC20 using TurboID.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:05:11.573.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	James Sipthorp
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-17 09:55:13	ID requested
1	2023-10-08 14:14:41	announced
⏵ 2	2024-10-22 06:05:11	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: TurboID, S-acylation, chemical proteomics, click chemistry,ZDHHC, ZDHHC20

Edward W. Tate
contact affiliation	Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, United Kingdom. The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom.
contact email	e.tate@imperial.ac.uk
lab head
James Sipthorp
contact affiliation	Imperial College London
contact email	james.sipthorp@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/2023/10/PXD032378

PRIDE project URI

• PRIDE
  1. PXD032378
     1. Label: PRIDE project
     2. Name: A palmitoyl transferase chemical genetic system to map ZDHHC-specific S-acylation