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DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2019-01-11
  • AnnouncementXML: Submission_2019-01-17_06:08:32.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Philip Brownridge
  • 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.
  • SpeciesList: scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; NCBI TaxID: 568708;
  • ModificationList: monohydroxylated residue; iodoacetamide derivatized residue
  • Instrument: Q Exactive

Dataset History

VersionDatetimeStatusChangeLog Entry
02018-09-10 02:10:32ID requested
12019-01-11 05:12:35announced
22019-01-17 06:08:33announcedUpdated publication reference for PubMed record(s): 30645593.

Publication List

  1. Canals R, Hammarlöf DL, Kröger 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]

Keyword List

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

Contact List

    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:

Full Dataset Link List

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