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Title: Using TraDIS to probe the model organism Escherichia coli
Author: Goodall, Emily C. A.
ISNI:       0000 0004 8499 6940
Awarding Body: University of Birmingham
Current Institution: University of Birmingham
Date of Award: 2019
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Transposon-directed insertion-site sequencing (TraDIS) is a high-throughput method that couples transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify the essential or conditionally essential genome of an organism, linking phenotype with genotype. A mini Tn5 transposon library was constructed in the model organism Escherichia coli K-12 strain BW25113. With a median distance between insertions of 3 bp, this is one of the most dense libraries published and provides a valuable tool for whole genome screening. Analysis of this library revealed subtle differences between the TraDIS method and the gold-standard gene-deletion method to determine the essential genome of an organism. This included, but was not limited to, the identification of transposon insertion bias, the boundaries of essential domains within a gene, and short essential domains within intragenic regions. Insertion bias was subsequently found to reveal the position of essential promoters and novel regulatory elements. This library was further used to probe the genomic requirement for survival in the presence of the clinically relevant antibiotic polymyxin B at sub-inhibitory concentrations. Among this data a gene of unknown function, yhcB, was identified and found to have a fundamental role in cell envelope biogenesis. The density of this library enabled identification of previously unreported genomic features. The results presented highlight the potential applications of TraDIS as a tool for a wide range of biological questions.
Supervisor: Not available Sponsor: BBSRC
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QH426 Genetics ; QR Microbiology