In antibiotic therapy design, conventional wisdom holds that higher antibiotic dosages always leads to the observation of fewer bacterial cells, resulting in a monotonic decay in cell number as a function of increasing antibiotic dose; accordingly, throughout this thesis, we will call this phenomenon a monotone dose-response profile. When we analysed the evolution of antibiotic resistance mediated by the multi-drug efflux pump AcrAB-TolC in Escherichia coli to study if such a monotone dose-response is maintained at all times, our analysis showed that higher dosages can, in fact, lead to higher bacterial loads. This is because selection for drug resistance is mediated by the duplication of the genes, AcrAB-TolC, that encode the aforementioned efflux pump. As explained in detail below, our work highlights the idea that Darwinian selection on additional copies of AcrAB-TolC is a non-linear function of antibiotic dose and that the observed transition from monotone to non-monotone dose-response is a consequence of AcrAB-TolC being strongly selected at very specific dosages. We term this phenomenon an ‘evolutionary hotspot’. Next, we extended the above experimental system to solid media to study how selection on resistance mediated by AcrAB-TolC leads to a ‘spatio-genomic patterning’ effect that we call a ‘bullseye’. Using a bespoke culture device developed as part of this PhD, we show that spatial selection on resistance also depends non-linearly on the distance of the cell from an antibiotic source, and that the non-linearity can be multi-modal as a function of distance, and therefore also of antibiotic dose. This result also contradicts the aforementioned principle that higher antibiotic dosages necessarily lead to fewer bacterial cells. Following on from this, we then studied the ability of microbial competitors for resources to modulate the antibiotic sensitivity of a particular strain of E. coli, namely Tets , using a range of multi-species experiments. We measured the sensitivity to antibiotics of Tets both with, and without, one bacterial or fungal competitor. When that competitor was equally sensitive to the antibiotic, we observed that Tets was less sensitive to it, in part due to an ‘antibiotic sinking’ effect carried out by the competitor strain. However, when the competitor was not sensitive to the antibiotic, Tets was, accordingly, more sensitive than in the absence of competition. In this latter case, the competitor seemed to reduce the growth of Tets by carbon theft as part of a phenomenon known as ‘competitive suppression’. Moreover, this ecological effect is one that synergises with the action of the antibiotic. Finally, we turned to a study of an ecological trade-off motivated by ribosome-binding antibiotics. So, by manipulating the content of ribosomal RNA in the E. coli cell, a large and essential molecule that is bound by antibiotics such as tetracycline or erythromycin, we could subsequently manipulate what is known as a metabolic trade-off between growth rate and growth yield. The latter is the number of cells produced per molecule of carbon found in the extracellular environment of the bacterial population. Using glucose as carbon source we therefore constructed an empirical fitness landscape that shows how the optimum number of ribosomal rRNA operons depends on extracellular glucose concentration. Whilst this study does not relate directly to the presence of an antibiotic, it does show that by altering the number of operons in a manner that is known to affect antibiotic susceptibility, we can also mediate important growth parameters like cell yield, aka efficiency, and growth rate.

published_or_final_version / abstract / Biochemistry / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Surgery / Doctoral / Doctor of Philosophy

published_or_final_version / Biological Sciences / Master / Master of Philosophy

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The lexA41 (formerly tsl-l) mutant was previously isolated as a UV-resistant, temperature-sensitive derivative of its UV-sensitive lexA3(Ind⁻) parent. Cells exhibit a so-called "split-phenotype", a phenomenon in which only a subset of the SOS responses can be detected physiologically following inducing treatments. In this work, lexA41 has been cloned and sequenced; the mutant gene retains the lexA3 mutation (Gly to Asp at position 85) and has a second mutation, lexA41 (Ala to Thr at position 132). LexA41 protein is not cleaved by the RecA protein-catalyzed pathway in vivo, but the mutant protein is degraded by the Lon protease at both 32° and 42°C. β-galactosidase activities of lac fusions to thirteen different SOS promoters were measured at 30° and 42° to determine levels of expression and were found to vary considerably. LexA41 protein is deficient in repressor function. The temperature sensitive phenotype is due to increased expression of sulA, which encodes a division inhibitor, at 42°. Excision repair genes, including uvrA, uvrB and uvrD, are constitutively expressed at 30° accounting for the UV resistance of the lexA41 mutant, but the SOS mutagenesis operon, umuDC, is not adequately derepressed explaining the failure to induce mutagenesis in this background. This differential expression of SOS genes gives a plausible explanation of the "split-phenotype" associated with lexA41. In another set of experiments, I have examined the level of expression of the SOS regulon in cells lacking DNA adenine methylase activity (dam⁻). Mud (Ap, lac) fusions to several SOS operons (recA, lexA, uvrA, uvrB, uvrD, sulA, dinD, and dinF) were found to express higher levels of (beta)-galactosidase in dam⁻ strains than in isogenic dam⁺ strains. The attempted construction of dam⁻ strains that were also mutant in one of several SOS genes indicated that viability of methylase-deficient strains correlates with the inactivation of the SOS repressor (LexA protein). Consistent with this, the wild-type functions of two LexA-repressed genes (recA and ruv) appear to be required for viability of dam⁻ strains.

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No description available.