Title: Connecting Cellular Redox State and Community Behavior in Pseudomonas aeruginosa PA14
Description: Redox chemistry is the basis for biological energy generation and anabolism. Redox conditions also serve as critical cues that modulate the development of many organisms. Roles for redox chemistry in the control of gene expression have been well characterized in multicellular eukaryotes, where oxygen availability in particular is a major developmental cue. As a gaseous metabolic substrate, oxygen becomes limiting as cellular communities grow, and can act as an indicator of aggregate size or developmental stage. In many of these cases, there are dedicated sensory and signal transduction networks that link oxygen and other redox signals to changes in gene expression and morphogenesis. The opportunistic pathogen Pseudomonas aeruginosa, like many species of microbes, forms multicellular structures called biofilms. Cells in biofilms can assume physiological states that differ from cells grown in well-mixed, homogeneous liquid cultures. They often exhibit increased resistance to environmental stresses and antibiotics, rendering biofilm physiology an important focus in the study of microbial pathogens.

Biofilm development and architecture are tuned by environmental conditions. In turn, growth and survival in the community, and the specific structure of that community, give rise to internal microenvironments that are experienced by cells within a biofilm. Mechanisms that tune biofilm developmental programs in response to redox conditions are not well understood. This is due to challenges presented by most popular laboratory models of biofilm formation, which are not amenable to perturbation, characterization at the microscale, or high-throughput screening or analysis. In this thesis, I describe a standardized colony morphology assay for the study of P. aeruginosa PA14 biofilm development and use this model to address fundamental questions about the relationships between electron acceptor availability, biofilm cell physiology, and the regulation of biofilm morphogenesis. In the colony morphology assay, PA14 grows as ~1cm-diameter biofilms on agar-solidified media under controlled conditions, and displays a developmental pattern that is predictably influenced by changes in redox conditions.

Microscale heterogeneity in chemical ecology can be profiled using microelectrodes, and the effects of specific mutations on development can be rigorously tested through high-throughput screening and the application of metabolic assays directly to biofilm samples. Prior to the work described here, application of the colony morphology assay had revealed that endogenous redox-active antibiotics called phenazines influence PA14 biofilm development such that defects in phenazine production promote colony wrinkling and the formation of a distinct wrinkle pattern. As phenazines can act as alternate electron acceptors for cellular metabolism, this provided an early clue to the role of redox conditions in determining biofilm architecture. The introduction to this thesis (Chapter 1) provides an overview of observations in P. aeruginosa and other microbes, drawing parallels between the physiology of colony biofilm development across phylogeny and highlighting specific preliminary studies that hint at redox-sensing mechanisms and signaling pathways that drive community morphogenesis.

The associated Appendix A examines the effects of CORM-2, a synthetic compound that releases the respiratory poison carbon monoxide, on P. aeruginosa biofilm development. The inhibitory effects of CORM-2 are ameliorated by reducing agents and increased availability of electron donors for P. aeruginosa metabolism. Chapter 2 describes the foundational characterization of the P. aeruginosa PA14 colony morphology assay model, which showed that colony wrinkling is invoked under high intracellular NADH levels and electron acceptor-limiting conditions, suggesting that it is an adaptive strategy to increase access to electron acceptor. The associated Appendices B and C describe (i) a mathematical modeling approach demonstrating that wrinkle geometry is indeed optimized for efficient access to electron acceptors, and (ii) a study investigating the effects of phenazine antibiotics on the multicellular development of a eukaryotic microbe. Chapter 3 details the identification and characterization of a candidate mediator of the multicellular response to electron acceptor availability in PA14 called RmcA.

RmcA contains domains that have been implicated in redox-sensitive developmental control in eukaryotic systems and domains that modulate intracellular levels of cyclic di-GMP (c-di-GMP). C-di-GMP is an important secondary messenger that controls social behaviors, including the secretion of factors required for colony biofilm structure formation, in diverse bacteria. RmcA thus bridges the gap between sensing of redox signals and colony morphogenesis. Appendix D outlines my approaches to purification and attempts to crystallize this and one other protein contributing to PA14 redox-driven colony morphogenesis. Finally, Appendix E describes the role of another protein that modulates c-di-GMP in response to metabolite-dependent signaling and physiological effects during interactions between P. aeruginosa and the fungus C. albicans. Together, the findings presented in this thesis have expanded our knowledge about the role that redox chemistry plays in biofilm development.