(6fz) Experimental Evolution of Heterologous Pathways in Microbes

Our ability to engineer microbial metabolic pathways is improving rapidly, enabling the efficient and sustainable biosyntheses of both bulk and fine chemicals. Tools from synthetic biology have supported these advances and allowed the use of diverse natural and engineered enzymes. However, novel enzymes frequently require significant optimization to function efficiently in a new production host. More precisely, optimization is a complex co-adaptation process, as the host must accommodate its new pathway and the pathway adjust to its new host. Many metabolic engineers seek to use rational and semi-rational strategies to predictably design highly-productive pathways in heterologous hosts. Unfortunately, these approaches are limited by our inability to account for the complexities involved in genome-scale engineering of microbial metabolism. When knowledge is limiting, evolutionary approaches can be powerful tools, both for forward optimization and as learning opportunities to investigate potential design strategies.

In my graduate research, I used RNA switches to perform directed enzyme evolution in live cells and systems biology to optimize an engineered microbe. My postdoctoral research has applied strategies from metabolic engineering to study natural microbial evolution, looking at how microbes evolve after horizontal gene transfer.

My independent research laboratory will investigate strategies for optimizing the interactions between a host and a novel enzyme or pathway using three related approaches. In my first project, I will extend my postdoctoral research to construct and optimize synthetic mobile genetic elements for bioremediation, effectively performing metabolic engineering in indigenous microbes. Next, I will study adaptation after horizontal gene transfer in a pathogen, looking at how previously-benign bacteria can evolve to become virulent. My final proposal describes a novel selection strategy using synthetic competitive ecosystems in microfluidic droplets. These ecosystems will be used to optimize complex pathways, such as those required to produce antibiotics, while studying the evolution of cooperation and competition in microbial communities. In combination, these projects will offer a novel perspective on important questions in health and ecology while also producing forward design strategies for synthetic biology and metabolic engineering.