PXD062881

PXD062881 is an original dataset announced via ProteomeXchange.

Title	Global analysis of protein degradation reveals instability of diverse regulators in Escherichia coli
Description	Regulated protein degradation underlies the timely execution of essential gene expression programs in bacteria. Here, we deployed time-resolved chemoproteomics, text mining of the PubMed and EcoCyc knowledge bases, and machine learning classification to discover proteolytic regulation in exponential and stationary phase Escherichia coli cultures. We experimentally validated the instability of diverse homeostatic and stress response regulators, including the principal cyclic-di-GMP phosphodiesterase PdeH, the N-end rule substrate chaperone ClpS, and all four A-type domain iron-sulfur cluster carriers, IscA, ErpA, NfuA, and SufA. Mutagenesis of the PdeH N-terminal extension abolished ClpXP recognition, which otherwise assisted in stationary phase depletion of PdeH. Unstable proteins synthesized in stationary phase such as the morphology regulator BolA, RNA polymerase ω subunit, and the biofilm regulator BssR were implicated in quiescence. Finally, machine learning–assisted substrate identification revealed Lon-mediated degradation of two opposing key regulators of surface adhesion, the RpoS antagonist FliZ and the major biofilm regulator CsgD, suggesting proteolysis may hasten transitions between motility and sessility. Together, these results highlight the role of regulated proteolysis in driving physiological adaptation for this model organism.
HostingRepository	PRIDE
AnnounceDate	2026-02-15
AnnouncementXML	Submission_2026-02-15_15:03:37.316.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD062881
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Elliot MacKrell
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-12 18:35:03	ID requested
⏵ 1	2026-02-15 15:03:37	announced

10.6019/PXD062881;

submitter keyword: None

Tsui-Fen Chou
contact affiliation	Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
contact email	tfchou@caltech.edu
lab head
Elliot MacKrell
contact affiliation	California Institute of Technology
contact email	ejmackrell@alumni.caltech.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/2026/02/PXD062881

PRIDE project URI

• PRIDE
  1. PXD062881
     1. Label: PRIDE project
     2. Name: Global analysis of protein degradation reveals instability of diverse regulators in Escherichia coli