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The Evolution of Microbial Metabolism on the Early Earth
Summary: Dianne Newman's research focuses on understanding the coevolution of microbial metabolism and the geochemistry of the Earth.
Electron transfer reactions are fundamental to metabolism. Whether an organism is autotrophic or heterotrophic, free living or an obligate parasite, every cell must solve the problem of energy generation in order to survive. At the cellular level, most of our knowledge of electron transfer comes from mechanistic studies of oxygenic photosynthesis and aerobic respiration, both in prokaryotic and eukaryotic systems. While today we know in exquisite detail the structure and function of various membrane-bound proteins involved in these electron transfer processes (such as cytochrome c oxidase in mitochondria), we know much less about the electron transfer agents of more ancient forms of metabolism. My laboratory is interested in the origin and evolution of the biochemical functions that characterize modern life on Earth, and we seek to develop ways of probing the coevolution of metabolism with Earth's near-surface environments. Understanding how modern microorganisms with archaic metabolisms function is a necessary step toward this end. Due to the basic nature of our questions, and the fact that many microenvironments on Earth today are anaerobic (such as the environments that characterize the majority of bacterial infections), this path of inquiry leads inexorably to insights about cellular electron transfer mechanisms that potentially have profound biomedical implications.
Because rocks provide the primary record of ancient events and processes, microbe-mineral interactions are our focus. In particular, we investigate how bacteria catalyze mineral formation, transformation, and dissolution, with a focus on how these processes are related to cellular energy generation and how they affect the geochemistry of their environment. For every metabolism that we study, we work with model organisms that we can genetically manipulate. Through a combination of classical genetic, biochemical, and molecular biological approaches, we identify the genes and gene products that control the processes of interest. For example, we have discovered how bacteria use sediment-bound arsenate as a terminal electron acceptor in anaerobic respiration and convert it to the more toxic and mobile form, arsenite; how anoxygenic photosynthetic bacteria utilize ferrous iron as an electron donor in photosynthesis and in the process precipitate rust anaerobically; and how magnetotactic bacteria control the production of chemically pure, single-domain magnetite (Fe3O4) within the magnetosome, a likely prokaryotic progenitor of eukaryotic organelles. Often, the bacteria that perform these reactions live together in biofilms, communities of cells attached to surfaces. Less exotic (but more virulent) bacteria also grow in biofilms, and therefore learning the rules of metabolism that govern life in these communities has tremendous clinical relevance. The following example illustrates this point.
Extracellular Electron Transfer to Iron Oxides
The Earth's geochemistry has changed substantially over time, in large part due to the influence of metabolic “inventions� by bacteria. A classic example of this is the evolution of photosystem II, which enabled cells to evolve molecular oxygen from water and thereby oxidize the Earth. Prior to this invention, however, for millions and perhaps billions of years, microbial life had to subsist anaerobically. How did cells cope? What electron acceptors and electron donors did they use for growth? It is increasingly accepted that ferric iron minerals may have been the most abundant and the most important terminal electron acceptors for ancient cellular respiration. Consequently, a large part of my group's research has been directed toward understanding how bacteria respire iron minerals such as poorly crystalline ferric (hydr)oxides [Fe(OH) 3] and goethite [α•FeOOH].
“Breathing� a mineral presents a challenge. Unlike most terminal electron acceptors that bacteria use for respiration (which are soluble and readily make their way to the cell to receive electrons from the membrane-bound molecules of the respiratory chain), ferric (hydr)oxide minerals are essentially insoluble under most environmental conditions. This means that simple dissolution and diffusion of ferric iron to the cell cannot be the answer. Somehow, the bacteria must deliver electrons to the mineral in such a way that they harvest energy in the process. We have shown that the bacterium Shewanella oneidensis excretes small organic molecules that mediate electron transfer from the cell to the goethite surface and consequently transform goethite to magnetite [Fe3O4]. Our work was the first to suggest that endogenous extracellular electron shuttles might be an important mechanism for mineral transformation by many different types of bacteria. Whereas previously it was thought that bacteria could only catalyze iron reduction through outer membrane cytochromes, requiring direct contact between the cell and the mineral, our results shifted the conceptual paradigm for this problem. Since then, our group and others have been attempting to determine the molecular basis for extracellular electron shuttling by different types of organisms. What are the structures of the shuttles and what is their evolutionary history? How important is this process in the environment? Do extracellular electron shuttles have any physiological function that transcends promoting iron reduction by mineral-respiring bacteria?
From Iron Oxides to Infections?
Recently, we have shown that redox-active antibiotics (e.g., phenazines and some glycopeptides) produced by common soil bacteria (e.g., Pseudomonas chlororaphis and Streptomyces coelicolor) and clinical isolates (e.g., Pseudomonas aeruginosa, an opportunistic pathogen of cystic fibrosis patients) can function as extracellular electron shuttles and can be exchanged between diverse bacterial species. (Figure 1 shows the structures of common phenazines.) In the presence of these antibiotics, the producer strains (as well as other organisms) rapidly reduce goethite to magnetite at rates that far exceed what happens in their absence. Intriguingly, the biosynthesis of phenazine antibiotics is up-regulated under conditions of high cell density and/or low oxygen tension, precisely the conditions that define a biofilm environment. Although my group has focused on electron shuttling in the context of mineral reduction, this is only one example in which extracellular electron transfer may be important. At the concentrations and under the conditions present in most natural environments, we hypothesize that production of extracellular electron shuttles might serve a basic physiological function for many biofilm-forming bacteria, beyond merely being “antibiotics.� Specifically, we have suggested that this function might be to promote iron acquisition and/or to facilitate energy generation for cells in biofilm communities. Testing this hypothesis will be a major goal of my lab's future research because, if true, it will have broad relevance for geobiology and medicine.
Given the paucity of information on biofilm metabolism and the evidence that extracellular electron shuttles such as phenazines may play a role in electron transfer metabolisms under conditions relevant for biofilms, we have recently begun to explore whether phenazines serve a physiological function for cells in biofilms, particularly in the context of P. aeruginosa infections. We are using biochemical, genetic, and physiological approaches to determine where in the cell phenazines are reduced, how they interface with the membrane-bound electron transfer chain, what genes are activated in their presence, and whether cells that produce them gain energy (for growth or maintenance) from their production and/or recycling. In addition, we are developing ways to measure directly when phenazines are made during the biofilm life cycle and how they affect its physiology (Figures 2 and 3).
This work has been supported by grants from the Office of Naval Research, the Defense Advanced Research Programs Agency, the Henry Luce Foundation, the Packard Foundation, and the Agouron Institute.
Last updated: January 11, 2006
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