PXD018422-2

PXD018422 is an original dataset announced via ProteomeXchange.

Title	Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein
Description	RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied to Salmonella enterica, GradR confirms many known RBPs by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinO-domain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element for building a comprehensive catalogue of microbial RBPs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:09:16.210.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Milan Gerovac
SpeciesList	scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; NCBI TaxID: 216597;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-07 22:33:46	ID requested
1	2020-07-16 02:50:53	announced
⏵ 2	2024-10-22 05:09:17	announced	2024-10-22: Updated project metadata.

Gerovac M, El Mouali Y, Kuper J, Kisker C, Barquist L, Vogel J, Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein. RNA, 26(10):1448-1463(2020) [pubmed]

10.1261/rna.076992.120;

submitter keyword: Salmonella, YafB, GradR, Hfq, CsrA, ProQ, FabA, RBP

Jörg Vogel
contact affiliation	Institute of Molecular Infection Biology, University of Würzburg, Würzburg Helmholtz Institute for RNA-based Infection Research, Würzburg
contact email	joerg.vogel@uni-wuerzburg.de
lab head
Milan Gerovac
contact affiliation	Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
contact email	milan.gerovac@uni-wuerzburg.de
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/2020/07/PXD018422

PRIDE project URI

• PRIDE
  1. PXD018422
     1. Label: PRIDE project
     2. Name: Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein