Metabolic Rewiring Promotes Bacterial Survival Under Oxidative and Reductive Stress

Author: Horak, Richard Davis

Year: 2026

Degree: Dissertation (Ph.D.)

Advisor: Newman, Dianne K.

Committee Members: Leadbetter, Jared R.; Ruby, Edward G.; Mazmanian, Sarkis K.; Newman, Dianne K.

Option: Microbiology

Abstract

Across the tree of life, all cells must follow unifying metabolic rules. Namely, organisms must balance electron flow to couple energy conservation with energy expenditure. Historically, studies in bacterial metabolism focused on exponential growth where cells are awash in nutrients and electron acceptors, exhibiting high bioenergetic levels. Therefore, from the perspective of both human biology and these fast-growing microbes, loss of redox balance is purely detrimental, leading to suppressed energetic states, growth arrest, and even death. Yet bacteria are commonly found under such conditions across diverse environments from industrial bioreactors to chronic infections to agricultural fields. This thesis was motivated by the remaining mystery behind how and why bacteria exist in such low energy survival states. Specifically, I focus on metabolic shifts during non-growth survival in the opportunistic pathogen Pseudomonas aeruginosa due to redox imbalance, as well as the potential benefits to such transitions. In the first section, I focus on oxidative stress, exploring bacterial survival during oxic nutrient starvation. I find that phenazines and toxoflavin – endogenous redox-active metabolites produced by P. aeruginosa and Burkholderia species respectively – lower the bioenergetic state of P. aeruginosa. Such bioenergetic self-poisoning would be traditionally deemed detrimental. Yet I find this phenomenon provides cells with increased tolerance to a variety of clinical antibiotics, suggesting cells might have agency over lowering their energetic state and that there is a benefit to doing so. In the following chapters, I turn my attention to reductive stress, examining the metabolic strategies P. aeruginosa uses to support anaerobic survival in the absence of terminal electron-acceptors. I discover that P. aeruginosa uses a phosphoketolase-mediated alternative glucose catabolic pathway under reductive stress, reminiscent of fermentative growth metabolisms in many obligate anaerobes. Moreover, this phosphoketolase plays a key role in mediating ribonucleotide homeostasis during survival-triggered macromolecule turnover. I find that many bacteria unable to grow in the absence of respiration contain phosphoketolases and show that at least two of these species, Dyella japonica and Paraburkholderia graminis, similarly rely on these enzymes for anaerobic survival. Finally, I speculate a generalizable role for phosphoketolases in supporting ribonucleotide turnover across bacterial taxa. These studies expose the large gaps remaining in our understanding of growth arrest metabolisms, even in well-studied model organisms. I hope this thesis motivates further exploration of these enigmatic yet important bacterial lifestyles.