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Title: Functional analysis of E. coli specific genes
Author: Thacker, Zubin
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2004
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The basis of my research has been to identify and characterise the function of ‘E. coli specific’ genes.  E. coli specific genes were identified after comparing 33 gamma proteobacterial genomes at the Microbial Genome Database (MBGD). The database was used to investigate the change in the number of E. coli specific genes since the completion of the first E. coli genome in 1997. Forty nine selected E. coli specific genes were deleted in 38 separate deletion events on the genome of the model E. coli K-12 MG1655 using the modified pKO3 deletion procedure. Gene expression levels and patterns in various phases of growth in LB broth were measured and are reported here.  Mutant and parent strains were tested for growth on a variety of conditions in agar based media. A mutant of the yigE ORF was found to be sensitive to high concentrations of nickel and cobalt in the growth medium. Mutation of the E. coli specific htrC gene showed no temperature sensitivity as reported in published literature and is shown here to play no part in the heat shock response of E. coli. The chromosomal position of the acetate utilisation gene ackB is experimentally demonstrated to be close to the known acetate kinase gene ackA at 50 minutes on the K-12 chromosome. Mutations in ORFs yceP, ydeK and ygjMN made the mutants sensitive to high levels of the basic dye gentian violet. This study shows that the group of genes specific to E. coli targeted here are expressed, show different patterns of expression and some are phenotypically functional. This study draws attention to a fraction of genes whose functional contribution to E. coli may have been underestimated due to their poor conservation in genomes other than E. coli.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available