Genome Engineering Technologies for Programming and Recoding Organisms

A defining cellular engineering challenge is the development of high-throughput and automated methodologies for precise design and manipulation of genomes. To address these challenges, we develop technologies – MAGE (multiplex automated genome engineering) and CAGE (conjugative assembly genome engineering) – for versatile genome modification and evolution of cells. Our methods treat the chromosome as both an editable and evolvable template and are capable of simultaneously targeting many locations on the chromosome to fundamentally re-engineer genomes from the nucleotide to the megabase scale without introducing mutagenic DNA double-strand breaks. I will first describe the use of these technologies to diversify pathways and recode genomes in bacteria. These Genomically Recoded Organisms (GROs) contain an alternative genetic code, in which all 321 UAG stop codons have been eliminated from the genome of E. coli. GROs exhibit improved properties for incorporation of nonstandard amino acids that expand the chemical diversity of proteins in vivo, establish genetic isolation and multi-virus resistance, and enable the engineering of GROs to depend on synthetic amino acids for robust biocontainment strategies. Finally, I will describe extensions of these genome engineering technologies into eukaryotic microorganisms. This work increases the toolbox for genomic and cellular engineering with the goal of expanding the functional repertoire of organisms.


Farren Isaacs is Associate Professor of Molecular, Cellular and Developmental Biology and Systems Biology at Yale University. He received a B.S.E in Bioengineering from the University of Pennsylvania and Ph.D. in Biomedical Engineering-Bioinformatics at Boston University, where he pioneered the development of synthetic RNAs capable of probing and programming cellular function. As a research fellow in genetics at Harvard, he invented enabling technologies for genome engineering. His research is focused on the development of genome engineering technologies to construct new genetic codes and for global reprogramming of cellular behavior to uncover new biological phenomena and expand the functions of living systems with applications in energy supply, environmental health, and medicine. He has been named a “rising young star of science” by Genome Technology Magazine, a Beckman Young Investigator by the Arnold and Mabel Beckman Foundation and recipient of a Young Professor award from DuPont.