Precise manipulation of chromosomes in vivo enables genome-wide codon replacement

Farren J. Isaacs, Peter A. Carr, Harris H. Wang, Marc J. Lajoie, Bram Sterling, Laurens Kraal, Andrew C. Tolonen, Tara A. Gianoulis, Daniel B. Goodman, Nikos B. Reppas, Christopher J. Emig, Duhee Bang, Samuel J. Hwang, Michael C. Jewett, Joseph M. Jacobson, George M. Church

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354 Citations (Scopus)

Abstract

We 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 32 Escherichia 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.

Original languageEnglish
Pages (from-to)348-353
Number of pages6
JournalScience
Volume333
Issue number6040
DOIs
Publication statusPublished - 2011 Jul 15

All Science Journal Classification (ASJC) codes

  • General

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    Isaacs, F. J., Carr, P. A., Wang, H. H., Lajoie, M. J., Sterling, B., Kraal, L., Tolonen, A. C., Gianoulis, T. A., Goodman, D. B., Reppas, N. B., Emig, C. J., Bang, D., Hwang, S. J., Jewett, M. C., Jacobson, J. M., & Church, G. M. (2011). Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science, 333(6040), 348-353. https://doi.org/10.1126/science.1205822