Genome-wide monitoring of gene knockouts and characterization of a new multidrug resistance operon

This dissertation is composed of two separate parts. In Project I, we developed a new genetic technique, MGK (for Monitoring of Gene Knockouts), which allows for the assessment of the relative fitness of thousands of knockout mutants in parallel. The utility of the method was established by applying it towards the identification of genes critical for fitness of bacteria grown in the absence of aromatic amino acids. MGK was able to identify all of the 13 Escherichia coli genes known to be essential for growth in media lacking these compounds. The flexibility of the approach was demonstrated by applying it toward analysis of two different E. coli gene knockout libraries: a random transposon insertion library and a defined gene deletion library. Comparison of the results obtained from both libraries demonstrated that MGK gave a more robust analysis when applied to the defined library. Overall, the results presented suggest that MGK can serve as a valuable tool in functional genomics studies applicable for rapid identification of new antibiotic targets.;In Project II, the methicillin resistant Staphylococcus aureus hospital isolate, CM05, was found to carry the genes encoding ribosomal RNA methyltransfases Erm(B) and Cfr located next to each other on the chromosome. Biochemical and genetic analyses of the transcriptional organization of erm(B) and cfr genes in the chromosome of the CM05 strain show that the two genes are organized into an operon, designated mlr (for modification of large ribosomal subunit), which is controlled by the erm(B) promoter. Analysis of the antibiotic inducibility of the erm (B) and cfr genes in the mlr operon suggests that neither of the two genes is subject to regulation by translation attenuation. Mutations found in the erm(B) leader open reading frame in the CM05 strain may account for the lack of induction. Further, we found that modification of A2503 independently decreases susceptibility to 16-member ring macrolides and synergistically enhances resistance conferred by modification of A2058 to this class of macrolides. Thus, the mlr operon contains two methyltransferase genes that are constitutively expressed and confers resistance to all protein synthesis inhibitors that target the large ribosomal subunit.