Katherine Petrie
kpetrie@scripps.edu

B.Sc. in Molecular Biology, Anthropology, and Japanese, 2006, University of Pittsburgh Research
with Profs. Roger Hendrix and Craig Peebles

Honors:
—Invited speaker, Gordon Research Conference on Origins of Life, 2008
—Phi Beta Kappa, 2006
—Dr. Norman Horowitz Fellow, University of Pittsburgh, 2006
—HHMI Summer and Academic Year Research Fellowships, University of Pittsburgh, 2004

Mentor:
Professor Gerald Joyce
Department: Molecular Biology

Research at TSRI:
Mutation and recombination provide the essential diversity upon which evolution acts. I have developed a new method for introducing random mutations during laboratory evolution. Molecular evolution in the laboratory is an iterative process of selection, amplification, and mutagenesis that recapitulates Darwinian evolution in vitro. It is a powerful technique used both as a tool to discover novel functional molecules and as an experimental model of evolving systems in nature. A current limitation of in vitro evolution, however, is that mutagenesis is performed as an isolated step, often in the form of occasional error-prone PCR. These sporadic bursts of diversification limit sequence exploration, and do not accurately reflect natural evolution, where mutations are continually introduced in concert with selection.

My approach integrates mutagenesis with selective amplification using mutagenic deoxynucleotide analogs during the continuous in vitro evolution of RNA ligase ribozymes. With these mutagenic analogs, mutations are introduced in every iteration of selection and amplification, so that diversity is constantly maintained. Using this integrated mutagenesis technique, I have demonstrated the emergence of an adaptive phenotype from a clonal starting population. I am currently using high-throughput Illumina sequencing technology to profile the mutation frequency and spectrum of the method, and hope to later use high-throughput sequencing to monitor evolving populations as mutations are introduced and selected.

My research aims to apply integrated mutagenesis to other laboratory evolution projects to enable the discovery of new sequence motifs and allow investigation of evolutionary dynamics. With the new mutagenesis method, I will carry out more exhaustive explorations of sequence space in the search for functionally significant ribozymes. I am also using integrated mutagenesis to examine the extent to which neutral mutations determine evolutionary trajectories. In both directions of research, I plan to couple integrated mutagenesis with an additional laboratory evolution technology – in vitro compartmentalization - to investigate the importance of environmental isolation in driving molecular change and to facilitate selection of trans-acting, intermolecular phenotypes.