Date of Award

2016

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Biochemistry & Molecular Biophysics

First Advisor

Rahul M. Kohli

Abstract

The ability of bacterial pathogens to evolve and adapt to our antimicrobial agents has precipitated a global health crisis where treatment options for bacterial infections are running low. Recently, studies have shown that the ability to acquire resistance is linked to the SOS response, which is a widely conserved network of genes involved in both high fidelity and error-prone DNA damage repair. The SOS response is regulated by the DNA-binding protein, RecA, and a repressor-protease, LexA. When the cell experiences stress, which can be caused by antibiotics, RecA polymerizes along single-stranded DNA and thereby stimulates LexA to undergo a conformational change and self-cleavage reaction (autoproteolysis). LexA self-cleavage de-represses downstream SOS genes, which are involved in both stress tolerance and mutagenesis. Various studies have shown that inactivating LexA autoproteolysis can both reduce the viability of bacteria under antibiotic stress and impede their ability to acquire resistance. These results therefore suggest that targeting LexA therapeutically could offer a novel way to combat the rise of resistance in pathogens, although to date no LexA inhibitors have been found. To facilitate the development of such therapeutics, we focused our efforts on examining LexA from 1) biochemical, 2) microbiological, and 3) drug discovery perspectives. On the biochemical front, we elucidated the substrate preference of LexA’s serine protease active site to form a better understanding of the target enzyme’s active site architecture. Performing saturation mutagenesis on the LexA’s internal cleavage loop, we showed that LexA possesses a unique active site, revealing residues involved in specific molecular recognition and conformational change. On the microbiological front, we examined how different LexA activities can impact bacterial drug susceptibility and stress-induced mutagenesis. Employing engineered E. coli strains with a spectrum of SOS activities, we showed that modulating LexA activity can increase bacterial susceptibility to antibiotics, while also tuning stress-induced mutagenesis. Finally, on the drug discovery front, we designed a high-throughput screen that enabled us to discover small molecule inhibitors of the LexA/RecA axis in collaboration with GlaxoSmithKline. Together, this work provides a multi-pronged foray into developing therapeutics that target the SOS pathway and combat the rise of antibiotic resistance.

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