Date of Award

2019

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Cell & Molecular Biology

First Advisor

Rahul M. Kohli

Second Advisor

Jay Zhu

Abstract

DNA damage is a pervasive environmental threat, as such, most bacteria encode a network of genes called the SOS response that is poised to combat genotoxic stress. In the absence of DNA damage, the SOS response is repressed by LexA, a repressor-protease. In the presence of DNA damage, LexA undergoes a self-cleavage reaction relieving repression of SOS-controlled effector genes that promote bacterial survival. However, depending on the bacterial species, the SOS response has an expanded role beyond DNA repair, regulating genes involved in mutagenesis, virulence, persistence, and inter-species competition. Despite a plethora of research describing the significant consequences of the SOS response, it remains unknown what physiologic environments induce and require the SOS response for bacterial survival. In Chapter 2, we utilize a commensal E. coli strain, MP1, and established that the SOS response is critical for sustained colonization of the murine gut. Significantly, in evaluating the origin of the genotoxic stress, we found that the SOS response was nonessential for successful colonization in the absence of the endogenous gut microbiome, suggesting that competing microbes might be the source of genotoxic stress. MP1 has an antimicrobial colicin under control of the SOS response, and colicins are hypothesized to function in inter-species competition. In Chapter 3, we therefore investigated the role of colicin in promoting successful colonization of MP1. We found that in the healthy murine gut, sustained colonization does not require colicin production, thus suggesting that MP1 existing in its natural niche does not face colicin-required microbial competition. This finding calls into question the importance of colicins in an unperturbed environment. Finally, with increased recognition of variance in SOS effectors across bacterial species, we posited that there may be a corresponding diversity in the regulatory LexA self-cleavage reaction. In Chapter 4, we systematically characterized LexA from phylogenetically-diverse bacterial species, uncovering a wide range of self-cleavage rates across bacterial species. Overall, this thesis describes non-canonical aspects of the SOS response by first exploring physiologic environments that require SOS activation, then investigating DNA repair-independent consequence of SOS induction, and finally probing the LexA self-cleavage reaction from multiple bacterial species.

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Microbiology Commons

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