CAREER: Quantitative Principles Governing the Cellular Metabolic Network

Princeton University, Princeton NJ

Investigators

Abstract

Cellular metabolism is a universal biological process, in which incoming nutrients are converted by cells into the energy and chemical building blocks that they need to survive and grow. It is carried out by a network of about 1000 interconnected chemical reactions. These reactions have been carefully mapped over the past century and have been found to be very similar across species ranging from bacteria to humans. With relatively complete maps of the metabolic network now in hand, there is the opportunity to begin to analyze the quantitative behavior of the entire system. Such analysis requires better tools for measuring the full spectrum of the system's components. The present research will develop methods for quantitating intracellular metabolite concentrations and fluxes using liquid chromatography - tandem mass spectrometry (LC-MS/MS), a state-of-the-art measurement technique. LC-MS/MS takes complex samples and separates them based on the individual components' physical properties and molecular weights, thereby allowing each component to be isolated and measured. The new measurement capabilities will be applied to determine the complete response of the unicellular model organisms Escherichia coli and Saccharomyces cerevisiae to environmental perturbations such as providing and removing fundamental nutrients. The metabolite concentration and flux responses will be used to guide the development of dynamic models of cellular metabolism. These models will begin to enable effective computational simulation of metabolic activity and its regulation. The broader impacts of this project include development of methods of probing metabolism of use to a wide range of investigators and identification of governing metabolic principles applicable also to bioengineering and mammalian biology. This research should lay the basic science groundwork to advance a diversity of applications, such as use of microorganisms to make alternative fuels and design of drugs to treat metabolic diseases like diabetes. The educational portion of the project aims to fill the unmet niche of providing a quantitative introduction to biochemistry for early stage undergraduates. It involves developing a new curriculum that integrates, around a central focus in metabolism, the teaching of biochemistry, organic chemistry, genetics, and elementary differential equations. The curriculum will include three core components: lectures, a textbook, and interactive computer-based exercises that walk students through the development of basic metabolic models. The effectiveness of the web-based exercises and lectures will be tested and refined through their classroom application, prior to codifying the material into a formal text and CD-ROM for students nationwide. The broader impact of this education effort will include training a diverse new generation of systems biology scientists. This will be achieved in two ways: by involving undergraduate and graduate students including underrepresented minorities in all stages of the research program and by developing a curriculum that engages undergraduates (at Princeton and nationwide) in quantitative biology early in their careers.