Editing the Genome: Scientists Unveil New Tools for Rewriting the Code of Life
ScienceDaily (July 15, 2011) — The power to edit genes is as revolutionary, immediately useful and unlimited in its potential as was Johannes Gutenberg's printing press. And like Gutenberg's invention, most DNA editing tools are slow, expensive, and hard to use -- a brilliant technology in its infancy. Now, Harvard researchers developing genome-scale editing tools as fast and easy as word processing have rewritten the genome of living cells using the genetic equivalent of search and replace -- and combined those rewrites in novel cell strains, strikingly different from their forebears.
Researchers have unveiled genome-engineering technologies capable of fundamentally re-engineering genomes from the nucleotide to the megabase scale. Treating the chromosome as both an editable and an evolvable template, the researchers have demonstrated methods to rewrite a cell's genome through powerful new tools for biotechnology, energy and agriculture. (Credit: iStockphoto/Zmeel Photography)
"The payoff doesn't really come from making a copy of something that already exists," said George Church, a professor of genetics at Harvard Medical School who led the research effort in collaboration with Joe Jacobson, an associate professor at the Media Lab at the Massachusetts Institute of Technology. "You have to change it -- functionally and radically."
Such change, Church said, serves three goals. The first is to add functionality to a cell by encoding for useful new amino acids. The second is to introduce safeguards that prevent cross-contamination between modified organisms and the wild. A third, related aim, is to establish multi-viral resistance by rewriting code hijacked by viruses. In industries that cultivate bacteria, including pharmaceuticals and energy, such viruses affect up to 20 percent of cultures. A notable example afflicted the biotech company Genzyme, where estimates of losses due to viral contamination range from a few hundred million dollars to more than $1 billion.
In a paper scheduled for publication July 15 in Science, the researchers describe how they replaced instances of a codon -- a DNA "word" of three nucleotide letters -- in 32 strains of E. coli, and then coaxed those partially-edited strains along an evolutionary path toward a single cell line in which all 314 instances of the codon had been replaced. That many edits surpasses current methods by two orders of magnitude, said Harris Wang, a research fellow in Church's lab at the Wyss Institute for Biologically Inspired Engineering who shares lead-author credit on the paper with Farren Isaacs, an assistant professor of molecular, cellular and developmental biology at Yale University and former Harvard research fellow, and Peter Carr, a research scientist at the MIT Media Lab.
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Science 15 July 2011:
Vol. 333 no. 6040 pp. 348-353 DOI: 10.1126/science.1205822REPORT
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Farren J. Isaacs1,*†‡, Peter A. Carr2,3,*‡§, Harris H. Wang1,4,5,6,*, Marc J. Lajoie1,7, Bram Sterling2,3,Laurens Kraal1, Andrew C. Tolonen1, Tara A. Gianoulis1,6, Daniel B. Goodman1,5, Nikos B. Reppas8, Christopher J. Emig9, Duhee Bang10, Samuel J. Hwang11, Michael C. Jewett1,12, Joseph M. Jacobson2,3, George M. Church1,6+
Author Affiliations
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.2Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.3MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.4Program in Biophysics, Harvard University, Cambridge, MA 02138, USA.5Program in Medical Engineering and Medical Physics, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.6Wyss Institute, Harvard University, Cambridge, MA 02115, USA.7Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA.8Joule Unlimited, Cambridge, MA 02139, USA.9Department of Bioengineering, Stanford University, Palo Alto, CA 94305, USA.10Department of Chemistry, Yonsei University, Shinchon 134, Seoul 120-749, Korea.11Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.12Department of Chemical and Biological Engineering and Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.+Author Notes↵† Present address: Department of Molecular, Cellular and Developmental Biology, Systems Biology Institute, Yale University, New Haven, CT 06520, USA.↵§ Present address: Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, MA 02420, USA.
‡To whom correspondence should be addressed. E-mail: farren.isaacs@yale.edu (F.J.I.); carr@mit.edu (P.A.C.)
* These authors contributed equally to this work.ABSTRACTWe present genome engineering technologies that are capable of fundamentally reengineering genomes from the nucleotide to the megabase scale. We used multiplex automated genome engineering (MAGE) to site-specifically replace all 314 TAG stop codons with synonymous TAA codons in parallel across 32Escherichia coli strains. This approach allowed us to measure individual recombination frequencies, confirm viability for each modification, and identify associated phenotypes. We developed hierarchical conjugative assembly genome engineering (CAGE) to merge these sets of codon modifications into genomes with 80 precise changes, which demonstrate that these synonymous codon substitutions can be combined into higher-order strains without synthetic lethal effects. Our methods treat the chromosome as both an editable and an evolvable template, permitting the exploration of vast genetic landscapes.
Received for publication 18 March 2011.
Accepted for publication 20 May 2011.
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