Yale iGEM Advances Innovation to World Stage

Yale Scientific Magazine | ysm@yale.edu December 5, 2012

The Yale iGEM Team’s key members: David Lim ‘13, Aaron Hakim ‘13, Jae Seong No ‘15, Aaron Lewis ‘14, Spencer Katz ‘13, and Andriana Lebid ’15. Courtesy of Aaron Lewis.

On October 12, team members Spencer Katz ‘13, Aaron Lewis ‘14, and David Lim ‘13, traveled to the International Genetically Engineered Machine (iGEM) Americas East Jamboree in Pittsburgh to win bronze medal standing and an invitation to the World Championship. The Yale iGEM team also earned Best Presentation Award, “beating even the team Queens Canada that brought a dozen dancers with them” according to Lewis. 2012 marks the third year of Yale’s participation in the undergraduate synthetic biology competition that aims to increase interest, research, and commercialization of biological engineering. The team began the summer with three ambitious projects, including microfluidics and the continuation of work with antifreeze proteins, but chose to focus on adaptation of Multiplex Automated Genomic Engineering (MAGE) to naturally competent bacteria.

MAGE is a process that drives synthetic evolution of E. coli. Recombineering achieved by MAGE involves targeted mutagenesis using single- or double-stranded DNA with regions of homology – complementary, matching DNA sequences – to specific sites on the bacterial genome. This exogenous, or new, DNA is incorporated with the aid of a “so-called” beta protein, and the organism’s disabled mismatch repair system prevents correction of generated mutations. Cycling of MAGE with specially-designed primers can consequently yield a diverse pool of bacteria which can be selected for desired traits.

MAGE can yield a diverse pool of bacteria, which can then be selected for desired traits. Courtesy of Professor Isaacs.

The MAGE technology acts by driving scores of genetic mutations during DNA replication, a mechanism conserved across all species from bacteria to humans. This year’s project not only aims to simplify the MAGE process with use of naturally competent bacteria, which takes up DNA with little manipulation, but also to expand the applicability of the mechanism. Whereas an electroporation step is laborious, time-consuming, and requires costly equipment in order to introduce exogenous DNA into E. coli during the MAGE cycling, the use of naturally competent B. subtilis and A. baylyi explored by the team would expand the scope, power, and accessibility of genome engineering. Also, the different bacterial strains may prove better systems for the expression of particular cellular products, creating potential for large industrial impact of MAGE and setting the stage for its development in other microbes, plants, and perhaps even humans.

Although facing occasional challenges, the Yale iGEM team is making steady progress. Having constructed a cassette, or a string of necessary genes for future experiments, and having established a plasmid library encoding various beta protein systems, the Yale iGEM team is on the brink of testing recombineering. Over the next few weeks, the team – with its key members also including Aaron Hakim ‘13, Andriana Lebid ‘15, and Jae Seong No ‘15, – will continue advancing the project. The World Championship will take place November 2 in Cambridge, Massachusetts.

Acknowledgements:
The Yale iGEM Team would like to thank everyone who has helped their efforts. Special thanks to Professor Farren Isaacs and graduate students in his lab as well as Professor Scott Strobel and Dr. Christoper Incarvito for permanent space on Yale’s West Campus.