Current Research and Scholarly Interests
Design and construction of synthetic genomes should enable powerful new approaches to the field of bioengineering and biotechnology applications, such as constructing new metabolic pathways in bacteria to synthesize medicines. However, due to the overwhelming complexity of biological systems, most designs to date have largely recapitulated natural sequences.
My research focuses on developing new methods of simplifying synthetic genomes. I chose to use a small lytic coliphage called phiX174 for my research. The intricate architecture of the circular 5.4 kb phiX174 genome encodes 11 gene products via highly overlapped protein coding sequences spanning multiple reading frames. The combination of small size and complexity makes the phiX174 genome an excellent test case.
Building synthetic phage genomes has been hampered in the past by the extreme toxicity of these viruses to E. coli. Recently, I developed a method that solves this problem by using yeast as a platform to assemble phiX174 genomes via homologous recombination (Jaschke PR, et al. 2012. Virology, in press). Using this method I have decompressed the phiX174 genome (i.e. separated all gene sequences), and showed that the virus is fully functional without gene overlaps.
My future goal is to pioneer a new method of simplifying synthetic genomes, a process I call 'negative genomics'. I will develop this method by systematically identifying and eliminating all cryptic DNA sequences from the phiX174 genome. Negative genomics will enable the building of more reliable and predictable synthetic genomes. Specifically, my work could facilitate concise engineering of bacteriophage genomes for improved diagnostics, next generation antimicrobials, and attenuated vaccines.