PXD011041

PXD011041 is an original dataset announced via ProteomeXchange.

Title	A multi-condition inter-strain transcriptomic compendium identifies phenotypic differences between European and African Salmonella pathovariants (C4PR_LIV)
Description	Salmonella Typhimurium ST313 is associated with invasive nontyphoidal salmonellosis (iNTS) disease in sub-Saharan Africa. Using ST313 isolate, D23580, and the well-characterized ST19 isolate 4/74, that causes gastroenteritis across Europe, we generated transcriptomic data from sixteen infection-relevant in vitro conditions and during infection of murine macrophages (http://bioinf.gen.tcd.ie/cgi-bin/jay/salcom_v2.pl?db=salcom_africa_new_HL). The transcriptional response of the two S. Typhimurium pathovariants to environmental stress was broadly similar. Comparative gene expression analysis identified virulence and metabolic genes that were up/down-regulated in D23580 versus 4/74. Findings were backed up by proteomic analysis, with12 genes being differentially-expressed at both the transcriptional and protein levels including melA and cysS. The data led us to discover that the ablation of melibiose utilization was caused by 3 SNP mutations in D23580 and to identify a novel plasmid-maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase. Our functional transcriptomic analysis represents a powerful tool for identification of key phenotypic differences between bacterial pathovariants.
HostingRepository	PRIDE
AnnounceDate	2019-01-11
AnnouncementXML	Submission_2019-01-17_06:08:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Philip Brownridge
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; NCBI TaxID: 568708;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-10 02:10:32	ID requested
1	2019-01-11 05:12:35	announced
⏵ 2	2019-01-17 06:08:33	announced	Updated publication reference for PubMed record(s): 30645593.

Canals R, Hammarl, ö, f DL, Kr, ö, ger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J, Monack DM, Kingsley RA, Brownridge P, Chaudhuri RR, Rowe WPM, Predeus AV, Hokamp K, Gordon MA, Hinton JCD, Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580. PLoS Biol, 17(1):e3000059(2019) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: RNA-seq, genomics, comparative transcriptomics, proteomics, plasmids, melibiose, tRNA synthetases, Salmonella Typhimurium, ST313, functional transcriptomics.

Jay C. D. Hinton
contact affiliation	Professor of Microbial Pathogenesis Institute of Integrative Biology Room 308, Biosciences Building, University of Liverpool Crown Street, Liverpool L69 7ZB, United Kingdom
contact email	jay.hinton@liv.ac.uk
lab head
Philip Brownridge
contact affiliation	University of Liverpool
contact email	philipjb@liv.ac.uk
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/2019/01/PXD011041

PRIDE project URI

• PRIDE
  1. PXD011041
     1. Label: PRIDE project
     2. Name: A multi-condition inter-strain transcriptomic compendium identifies phenotypic differences between European and African Salmonella pathovariants (C4PR_LIV)