Date of Award


Degree Type


Degree Name

Doctor of Philosophy in Biological and Environmental Sciences


Cell and Molecular Biology


Cell & Molecular Biology

First Advisor

Jodi L. Camberg


Responding to environmental stress is critical for all organismal survival, including in bacteria. One of the key bacterial responses to stress is protection of proteins within the cell, which helps to maintain proteins in a functional state. Protection of the proteome is done through a collaborative network of proteins and systems, all functioning to protect the cell. Within Escherichia coli (E. coli), three main proteomic protection systems are chaperones, proteases, and toxin-antitoxin (TA) systems. They work together, with overlapping functions, to regulate stress responses. Chaperones, such as DnaK(Hsp70) and SecB, are major regulators of protein folding within the cell, assisting to keep proteins folded during stress or refolding misfolded proteins. Cellular proteases like, ClpXP and Lon, degrade substrate proteins to alter their intracellular concentration or remove misfolded proteins from the proteomes. Toxin-antitoxin (TA) systems regulate growth during periods of stress by freeing cellular toxin to compromise key cellular processes.

In Manuscript I, I discuss the roles and functions of TA systems in E. coli by reviewing the eight different types of TA systems. I break down the differences between the types and expand on type II TA systems, the most well-studied system. I then discuss the mode of activation for type II TA systems and the proteases and chaperones that regulate TA function.

In Manuscript II, we report on the regulation of the E. coli MqsRA TA system by the ClpXP protease in vitro. We discover the binding sites on both ClpX and MqsA that mediate this interaction, how the occupancy of zinc by MqsA alters its regulation, and we propose a model for how MqsA is regulated by proteases during stress to free toxin.

In Manuscript III, we discover a novel mechanism for MqsA regulation during periods of stress by monitoring MqsA levels in vivo. We report how MqsA is regulated by proteases in vivo and how this interaction is altered during stress. We also report on a novel mechanism for the SecB chaperone in regulating MqsA levels, how this regulation translates to proteolysis in vitro and during translation of nascent MqsA. Lastly, we investigate ribosome nascent chain (RNC) complexes containing MqsA and discover regulation by proteases and chaperones.

In conclusion, we report regulatory interactions between ClpXP and MqsA that underpin MqsR toxin activation, we discover a novel regulatory mechanism for MqsA and SecB, and investigate a model of co-translational regulation of MqsA as a function of the stress response. Altogether, this work reveals novel regulatory mechanisms for TA system activation, regulation at the ribosome, proteolysis, and the cellular stress response.

Available for download on Wednesday, May 08, 2024