PXD034373-1

PXD034373 is an original dataset announced via ProteomeXchange.

Title	Identification of bile acid-interacting proteins in Salmonella Typhimurium (14028S) by chemoproteomics
Description	The microbiota generates structurally diverse small molecules that can regulate host physiology and disease. Of these microbiota metabolites, bile acids have emerged as important modulators of host immunity and microbial pathogenesis. While the modes of action for different bile acids on host pathways are becoming more apparent, the mechanisms by which these prominent microbiota metabolites suppress microbial virulence pathways are less clear. To identify the direct protein targets of bile acids in Salmonella, we have generated three photoaffinity bile acid reporters (alk-X-CDCA, alk-X-UDCA, alk-X-LCA) and performed chemical proteomics. Using a combination of photocrosslinking with bile acid chemical reporters and label-free proteomics, we performed a quantitative analysis of bile acid interacting proteins in Salmonella with or without UV-mediated photocrosslinking. These studies revealed bile acid can interact with many Salmonella proteins, such as extracellular or secreted proteins, T3SS components and motility-related proteins, as predicted by Gene Ontology analysis. In addition, cytoplasmic and membrane proteins including metabolic enzymes are also identified. Notably, HilD, an important transcriptional regulator of S. Typhimurium virulence was also identified by the alk-X-CDCA reporter. This study highlights the utility of chemical proteomics to identify the direct protein targets and mechanisms of action for microbiota metabolites in bacterial pathogens.
HostingRepository	PRIDE
AnnounceDate	2022-09-29
AnnouncementXML	Submission_2022-09-28_19:50:47.872.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xinglin Yang
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028; NCBI TaxID: 1299114;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-06 06:40:33	ID requested
⏵ 1	2022-09-28 19:50:48	announced
2	2023-11-14 08:56:18	announced	2023-11-14: Updated project metadata.

10.1038/S41589-022-01122-3;

submitter keyword: Bile acids, Salmonella, chemoproteomics, photoaffinity

Howard C. Hang
contact affiliation	Departments of Immunology & Microbiology and Chemistry Scripps Research
contact email	hhang@scripps.edu
lab head
Xinglin Yang
contact affiliation	Scripps Research
contact email	xiyang@scripps.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/2022/09/PXD034373

PRIDE project URI

• PRIDE
  1. PXD034373
     1. Label: PRIDE project
     2. Name: Identification of bile acid-interacting proteins in Salmonella Typhimurium (14028S) by chemoproteomics