To survive in changing environments, organisms must acquire new traits. However, mechanisms that protect the genome generally limit genome modifications to small changes in DNA sequence. Given this paradox, how do organisms adapt to new conditions? One way to study this question is with prions. Prion proteins adopt multiple conformations (or shapes), and these unusual and diverse conformations drive a paradigm-shifting mode of inheritance that is based on changes in protein shape rather than changes in DNA sequence. Although best known as the cause of mad cow disease, the majority of the nearly two-dozen prions that have now been identified are benign or beneficial. One such prion, termed [GAR+], controls a fundamental decision in metabolism: whether to harvest energy by breaking down glucose in the absence of oxygen (fermentation) or to harvest energy through the breakdown of glucose (or other organic substrates)in the presence of oxygen (respiration). This metabolic switch between fermentation and respiration has been associated with a diverse array of disease states. It was recently discovered that many bacteria secrete small molecules that induce the [GAR+] prion in neighboring eukaryotic cells. Mathematical modeling suggests that both organisms derive benefit from this interaction in some circumstances. However, this interaction can disrupt industrially important fermentation processes and may be harmful to human health. The recent recognition that the microorganisms associated with an organism are often correlated with certain disease states suggests that lessons we learn from better understanding the interactions between prion proteins and bacteria will have broad significance. Therefore, this project will characterize the interactions between bacteria and yeast that result in prion acquisition, and work to identify the compound(s) produced by bacteria that induces the prion. The experimental methods and data analysis approaches developed will be useful for studying a variety of systems, and the results will be transmitted to the public through peer-reviewed publications and training of high school, undergraduate, and graduate students. Undergraduate and high school students and teachers will be introduced to the scientific process and will be taught how to design experiments in quantitative cell and molecular biology. High school students will be recruited for a "boot camp" style course that will include developing teaching modules, training of K-12 science teachers, and working with Stanford University's Center for Teaching and Learning. Undergraduate students will be recruited for the project from existing programs that focus on students from underrepresented backgrounds (including Stanford Amgen-SSRP Scholars Program). A two-week "Methods and Logic in Chemical and Systems Biology Boot Camp" for incoming graduate students will be developed which will teach inquiry-based learning and directly integrate concepts and experiments from the project.
Adaptation to changing environments requires the rapid acquisition of new heritable traits, generally ascribed to mutations. However, epigenetic mechanisms can also generate phenotypic diversity among genetically identical cells. Among these mechanisms, self-perpetuating protein conformations, known as prions, are emerging as an important means of generating phenotypic diversity that is heritable from one generation to the next. Recent studies suggest that these elements are common in wild fungi, where they often confer adaptive traits. An ancient biological circuit in fungi and many other eukaryotes normally prevents the use of other carbon sources when glucose is present. The [GAR+] prion reverses yeast's strong glucose repression. Although organisms have largely been studied in isolation, in the wild they compete and cooperate in complex communities, and it was recently discovered that bacteria can secrete a chemical factor that elicits the [GAR+] appearance. This induction can provide strong benefits to yeast and bacteria alike. Bacteria benefit because [GAR+] yeast produce less ethanol, creating a less toxic environment. [GAR+] yeast benefit from enhanced growth on mixed carbon sources and greater longevity. Four specific aims will investigate this novel interspecies interaction and the ensuing heritable shift in metabolism: 1) Identify and characterize genes that control interspecies communication, 2) Identify the bacterial signal that induces the [GAR+] prion, 3) Investigate how [GAR+] influences cooperation and cheating in mixed populations, and 4) Characterize mechanisms that drive the [GAR+] metabolic switch using systems-level approaches. Although dozens of prions have been discovered in the past decade, we lack understanding of their physiological consequences and of factors that regulate their acquisition and loss. This research will employ novel methods to dramatically enhance our understanding of what is emerging as a conserved and fundamental biological process. The experimental methodology and data analysis platforms developed will be useful for studying a variety of systems, and will lead to new insights into how a prion can heritably transform one of the most fundamental decisions in metabolism, and in particular how such regulatory decisions can be fueled by cross-kingdom chemical communication.
