Emily Wrenbeck - Graduated summer 2017
The focus of my PhD research was to gain better understanding of the constraints of functional enzyme evolution using a research technology pipeline developed by the Whitehead Lab. In brief, the pipeline involved coupling high-throughput screens or selections for protein function to deep sequencing to generate datasets containing information on thousands of mutations of a protein sequence. This was applied to study how enzymes encode substrate specificity, which is currently not well understood, by performing functional selections for an enzyme on multiple substrates. In this work, I found that specificity is globally encoded throughout protein sequence and structure. In addition, during my PhD I co-developed Nicking Mutagenesis, a method for the construction of comprehensive single-site saturation mutagenesis DNA libraries that requires only double-stranded plasmid DNA as input substrate. This method was validated on several gene targets and plasmids and is currently being used in academic, government, and industry laboratories worldwide.
During my time in the training program I was exposed to new areas of research and ways of thinking that undoubtedly influenced my scientific interests and career goals. Specifically, from the material covered in program courses and the lectures given by invited speakers at the annual symposia I became captivated with the idea of biomanufacturing and natural product synthesis in engineered microbes. This led me to pursue a related research project and ultimately to a collaboration between the Whitehead Lab (Dept. of Chemical Engineering) and the Barry Lab (Dept. of Horticulture and another training lab). In brief, this project entailed applying the research pipeline to engineer improved heterologous expression of an enzyme from the Atropa belladonna medicinal Tropane Alkaloids pathway recently discovered by the Barry Lab, with the ultimate goal of improving productivity of an engineered Tropane Alkaloids biosynthetic pathway in yeast. These program-inspired interests will be continued this fall when I begin my career as a scientist at Ginkgo Bioworks (Boston, MA) with the title of Protein Engineer. I hope to expand my knowledge of natural product synthesis and state-of-the-art technologies for engineering biology, be part of developing a world-class protein engineering group, and glean insight into the business workings of a biotechnology company.