PXD032725

PXD032725 is an original dataset announced via ProteomeXchange.

Title	System-wide analyses reveal essential roles of N-terminal protein modification in bacterial physiology
Description	Removal of the N-terminal formyl group on nascent proteins by peptide deformylase (PDF) is the most prevalent protein modification in bacteria that impacts over 90% of the proteome. PDF is essential and a critical target of antibiotic development; however, its role in bacterial physiology remains a long-standing question. In this work, we used system-wide and time-resolved analyses of the E. coli translatome and proteome to investigate the consequences of PDF inhibition at different stages. We found that PDF inhibition results in the rapid activation of cellular stress responses, especially those associated with defects in protein folding and perturbations at the bacterial inner membrane, followed by a global downregulation of metabolic pathways. Functional assays reveal the rapid hyperpolarization of the plasma membrane and impaired membrane integrity upon PDF inhibition, suggesting that disruption of plasma membrane is the most immediate and primary consequence of formyl group retention on nascent proteins. Our work resolves the physiological function of a ubiquitous N-terminal protein modification and uncovers its crucial role in maintaining the proper structure and function of the bacterial membrane.
HostingRepository	PRIDE
AnnounceDate	2022-07-20
AnnouncementXML	Submission_2022-07-20_08:52:17.337.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeff Jones
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	acetylated residue; formylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-23 07:02:04	ID requested
⏵ 1	2022-07-20 08:52:17	announced

10.1016/J.ISCI.2022.104756;

submitter keyword: protein biogenesis, N-terminal protein modification, peptide deformylase, mass spectrometry, ribosome profiling, membrane potential

Tsui-Fen Chou
contact affiliation	Faculty Director, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
contact email	tfchou@caltech.edu
lab head
Jeff Jones
contact affiliation	California Institute of Technology
contact email	jeffj@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/2022/07/PXD032725

PRIDE project URI

• PRIDE
  1. PXD032725
     1. Label: PRIDE project
     2. Name: System-wide analyses reveal essential roles of N-terminal protein modification in bacterial physiology