PXD026488-1

PXD026488 is an original dataset announced via ProteomeXchange.

Title	Monitoring Fe-S cluster occupancy across the E. coli proteome using chemoproteomics
Description	Iron-sulfur (Fe-S) clusters are ubiquitous metallocofactors involved in redox chemistry, radical generation, and gene regulation. Common methods to monitor Fe-S clusters include spectroscopic analysis of purified proteins, and auto-radiographic visualization of radiolabeled iron distribution in proteomes. Here, we report a chemoproteomic strategy that monitors changes in the reactivity of Fe-S cysteine ligands to inform on Fe-S cluster occupancy. We highlight the utility of this platform in E. coli by: (1) demonstrating global disruptions in Fe-S incorporation in cells cultured under iron-depleted conditions; (2) determining Fe-S client proteins reliant on three scaffold/carrier proteins within the Isc Fe-S biogenesis pathway; and, (3) identifying two previously unannotated Fe-S proteins, TrhP and DppD. In summary, the chemoproteomic strategy described herein is a powerful tool that reports on Fe-S cluster incorporation directly within a native proteome, and enables the interrogation of Fe-S biogenesis pathways, and the identification of previously uncharacterized Fe-S proteins.
HostingRepository	PRIDE
AnnounceDate	2024-05-22
AnnouncementXML	Submission_2024-05-22_03:07:54.054.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniel Bak
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	iodoacetamide derivatized amino-terminal residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-04 06:01:12	ID requested
⏵ 1	2024-05-22 03:07:54	announced
2	2024-10-22 06:41:18	announced	2024-10-22: Updated project metadata.

Bak DW, Weerapana E, Monitoring Fe-S cluster occupancy across the E. coli proteome using chemoproteomics. Nat Chem Biol, 19(3):356-366(2023) [pubmed]

10.1038/s41589-022-01227-9;

submitter keyword: ReDiMe, Iron-sulfur clusters, isoTOP-ABPP,E. coli

Eranthie Weerapana
contact affiliation	Chemistry Department, Boston College, USA
contact email	eranthie@bc.edu
lab head
Daniel Bak
contact affiliation	Boston College
contact email	bakd@bc.edu
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/2024/05/PXD026488

PRIDE project URI

• PRIDE
  1. PXD026488
     1. Label: PRIDE project
     2. Name: Monitoring Fe-S cluster occupancy across the E. coli proteome using chemoproteomics