Search

Studying bacterial physiology is crucial to understand the fundamental mechanisms that govern bacterial growth, survival, and adaptation. This thesis combines two chapters investigating bacterial physiology by studying important cellular processes like bacterial toxin-antitoxin systems and proteolytic pathways. The first chapter involves studying bacterial toxin-antitoxin systems to understand the regulation and function of hypothetical toxin-antitoxin (TA) systems of bacteria and the effects of these TA systems on bacterial growth and survival. The emergence of these genetic modules in bacterial research and the unrevealing of some of their important roles in cell physiology in recent years has drawn much attention in scientific communities. This chapter looks for new TA systems using molecular techniques and conventional microbiology approaches. The results of this study show the effects of a toxin protein of the putative YfeD-YfeC TA system of Escherichia coli (E. coli). The second chapter utilizes a systems biology approach by using molecular biology, synthetic biology, and RNA-Seq techniques to understand the effect of artificial proteolytic queueing in E. coli by introducing synthetic degradation circuits into them. The goal of this project was to test if the formation of an artificial proteolytic queue alters gene regulation. Our results demonstrate that the artificial proteolytic queue causes a cellular burden. Furthermore, this burden does not slow growth because the cell mitigates the queueing effect by responding to it by upregulating specific genes; specifically, chaperones and proteases.