Reprogramming Cells with Plant-Derived Signaling Pathways

Trillions of individual cells are coordinated in multicelled organisms to perform complex functions such as chemical processing, movement, and even the processes of thought. Each cell can send and receive a variety of signals and act on the received information to play the appropriate role within the whole. Although examples abound in nature, engineering complex multicelled systems to desired specifications is not currently possible. These Allen Distinguished Investigators have devised a project inspired by two interconnected questions: (1) How do cells process information (such as where they are within the organism, what is happening in their environment), and (2) Can we use biological parts and cellular logic to engineer new systems with useful behaviors (such as generating new organs, making fuel). Specifically, this research project is reverse-engineering responses to the plant hormone auxin – central to nearly every aspect of higher plant life and evolution – into baker's yeast. Yeast is a single-celled genetic powerhouse that facilitates rapid, quantitative assays on the behavior of individual cells over time. Once the auxin system is rebuilt in yeast, researchers will learn to program with it. The results will provide new tools for engineering multicelled systems and also generate models for how and why auxin is used so effectively by plants.

Affiliated Investigators

Eric Klavins, Ph.D.

University of Washington

Eric Klavins is an associate professor of electrical engineering at the University of Washington in Seattle. He received a B.M. in Music in 1992 and a B.S. in computer science in 1996 from San Francisco State University. He received the M.S. and Ph.D. degrees in computer science and engineering in 1999 and 2001 from the University of Michigan, Ann Arbor. From 2001 to 2003 he was a postdoctoral scholar in the Control and Dynamical Systems Department at the California Institute of Technology where he worked with Richard Murray. In 2003 Eric was hired in Electrical Engineering at the University of Washington in Seattle, WA and received tenure in 2009. He holds adjunct appointments in Computer Science and Engineering and in Bioengineering and is the Director for the UW Center for Synthetic Biology.

Until approximately 2008, Klavins' research was primarily in computer science and control systems, focusing on stochastic processes, robotics and self-assembly. At about this time, he learned the basics of genetic engineering and for the next few years switched fields entirely to synthetic biology and now runs an interdisplinary group of engineers, biologists, experimentalists, and theorists -- all focused on engineering life. His current projects include synthetic multicellular systems with engineered bacteria and yeast, modeling and design for synthetic multicellular systems, and laboratory automation.

Jennifer Nemhauser, Ph.D.

University of Washington

Jennifer Nemhauser is a Professor in the Department of Biology at the University of Washington. She is interested in plant growth networks, and in particular the small-molecule triggered signaling pathways that integrate information from the environment, developmental programs and metabolism. Jennifer started her research career as a technician in Eric Lander’s lab (then at the Whitehead Institute)—an experience that imprinted her with a love for that sweet spot where novel quantitative approaches, new technology and really-challenging biological questions meet-up. As a graduate student at the University of California with Pat Zambryski, Jennifer got hooked on the big question of how cells figure out where they are during development. She discovered that the plant hormone auxin played a pivotal role in relaying this type of information in a highly context-dependent manner. Her postdoctoral work with Joanne Chory at the Salk Institute allowed Jennifer to use first-generation genomic tools to begin building an organismal, integrated view of plant signaling and development. This adventure continues in her own lab, where she has teamed up with Eric Klavins, a UW Associate Professor of Electrical Engineering and fellow Allen Distinguished Investigator, to recreate auxin signaling in yeast—using synthetic biology paradigms to ground-truth the predictions generated by systems-level approaches.