PXD018754

PXD018754 is an original dataset announced via ProteomeXchange.

Title	A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
Description	Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of characterization in microbes other than Escherichia coli. Here, we have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (TraDIS), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrated a virulence and motility defect of a Salmonella ΔmgrB mutant and revealed an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Overall, our study highlights the power of interpreting available “omics” datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.
HostingRepository	PRIDE
AnnounceDate	2020-12-07
AnnouncementXML	Submission_2020-12-07_00:49:40.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Maass
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Typhimurium; NCBI TaxID: 90371;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-23 01:02:56	ID requested
⏵ 1	2020-12-07 00:49:41	announced

Dataset with its publication pending

submitter keyword: small proteins, Salmonella Typhimurium, dual RNA-seq, TraDIS, Grad-seq, Ribo-seq, sPepfinder, MgrB, virulence, infection, host-pathogen interaction

Dörte Becher
contact affiliation	Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
contact email	dbecher@uni-greifswald.de
lab head
Sandra Maass
contact affiliation	University of Greifswald, Department for Microbial Proteomics
contact email	sandra.maass@uni-greifswald.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/2020/12/PXD018754

PRIDE project URI

• PRIDE
  1. PXD018754
     1. Label: PRIDE project
     2. Name: A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence