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Katherine Petrie




Katherine Petrie

Graduate Student
August 2006 – present
BPhil and BA, 2006, University of Pittsburgh
Research: Evolutionary fitness landscapes 
E-mail: kpetrie@scripps.edu

 

Darwinian evolution accounts for the remarkable diversity and complexity of life on Earth. It also governs the emergence of drug resistance and the progression of cancer. Despite evolution’s central importance to biology, scientists are unable to predict and explain what genotypic and phenotypic changes are accessible during the course of evolution. In vitro evolution enables researchers to observe these genotypic and phenotypic changes under controlled laboratory conditions.

Continuous in vitro evolution is a technique developed by the Joyce laboratory in which RNA enzymes are selectively amplified on the basis of their enzymatic activity. Among a diverse population of RNA enzymes, those individuals with the highest activity (highest fitness) are replicated the fastest, and can grow to dominate the population. In this competitive system, variant RNA enzymes that arise through mutation may be lost, persist, or increase in frequency, depending on how the mutations affect relative fitness. It is possible to observe ten generations of continuously evolving RNA enzymes in just a few hours, allowing one to witness the course of evolutionary history.

The ‘genome’ of the continuously evolving RNA enzymes contains only about 200 nucleotides. This enables the use of next-generation sequencing technology to examine millions of individuals from the evolving population, tracking changes in the abundance of particular genotypes and revealing preferred evolutionary trajectories. To exhaustively examine potential genotypes, massively parallel in vitro evolution experiments are being carried out using microfluidic water-in-oil emulsions to isolate individual founder molecules within separate compartments. These experiments are expected to reveal how factors such as mutation rate and selection stringency determine what genotypes can be discovered by evolution when populations are subject to genetic drift. These insights may help researchers better understand and predict evolution in natural populations.

Also under study is the role of mutability. During continuous evolution, mutagenic deoxynucleotide analogs are included in the amplification step to maximize diversity. It might have been expected that such mutagens would induce random mutations throughout the RNA enzyme, but this was not the case. In a single amplification step, prior to the effects of selection, the mutation rate was found to vary dramatically across the RNA sequence. Local sequence features appear to be critical in determining the tolerance of particular nucleotide positions to mutation. This implies that fitness alone may not be the sole determinant of which genotypes are accessible during evolution – the mutability of particular sequences also may shape evolutionary pathways.

Petrie Figure 1

A model fitness landscape. Individual genotypes connected by mutation are plotted against their fitness in a landscape representation. By tracking the abundance of individual genotypes during in vitro evolution, it will be possible to map which evolutionary trajectories are most readily accessible.

Petrie Figure 2

Compartmentalized evolution and the founder effect. A microfluidic device is used to generate water-in-oil emulsions where in vitro evolution is carried out in millions of separate aqueous compartments. Evolution is initiated from a single unique sequence in each compartment to exploit the founder effect and allow genetic drift to occur.

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