A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

Salmonella Typhi and Typhimurium diverged only ∼50 000 years ago, yet have very different host ranges and pathogenicity. Despite the availability of multiple whole-genome sequences, the genetic differences that have driven these changes in phenotype are only beginning to be understood. In this study...

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Published inNucleic acids research Vol. 41; no. 8; pp. 4549 - 4564
Main Authors Barquist, Lars, Langridge, Gemma C, Turner, Daniel J, Phan, Minh-Duy, Turner, A Keith, Bateman, Alex, Parkhill, Julian, Wain, John, Gardner, Paul P
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.04.2013
Subjects
Bacterial Proteins - genetics
DNA Transposable Elements
Gene Library
Genes, Bacterial
Genomics
Mutagenesis, Insertional
RNA, Small Untranslated - genetics
RNA, Untranslated - genetics
Salmonella typhi - genetics
Salmonella typhi - growth & development
Salmonella typhimurium - genetics
Salmonella typhimurium - growth & development
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Summary:Salmonella Typhi and Typhimurium diverged only ∼50 000 years ago, yet have very different host ranges and pathogenicity. Despite the availability of multiple whole-genome sequences, the genetic differences that have driven these changes in phenotype are only beginning to be understood. In this study, we use transposon-directed insertion-site sequencing to probe differences in gene requirements for competitive growth in rich media between these two closely related serovars. We identify a conserved core of 281 genes that are required for growth in both serovars, 228 of which are essential in Escherichia coli. We are able to identify active prophage elements through the requirement for their repressors. We also find distinct differences in requirements for genes involved in cell surface structure biogenesis and iron utilization. Finally, we demonstrate that transposon-directed insertion-site sequencing is not only applicable to the protein-coding content of the cell but also has sufficient resolution to generate hypotheses regarding the functions of non-coding RNAs (ncRNAs) as well. We are able to assign probable functions to a number of cis-regulatory ncRNA elements, as well as to infer likely differences in trans-acting ncRNA regulatory networks.
Bibliography:The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
John Wain, Norwich Medical School, University of East Anglia, NRP Innovation Centre, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7GJ, UK.
Paul P. Gardner, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
Present addresses: Daniel J. Turner, Oxford Nanopore Technologies, Oxford, OX4 4GA, UK.
A. Keith Turner, Discuva Ltd., 260 Cambridge Science Park, Milton Road, Cambridge, CB4 0WE, UK.
Minh-Duy Phan, Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkt148