Design, synthesis, and testing toward a 57-codon genome

Nili Ostrov(Harvard University), Matthieu Landon(Harvard University), Marc Güell(Harvard University), Gleb Kuznetsov(Harvard University), Jun Teramoto(Harvard University), Natalie Cervantes(Harvard University), Minerva Zhou(Massachusetts Institute of Technology), Kerry Singh(Massachusetts Institute of Technology), Michael G. Napolitano(Harvard University), Mark Moosburner(Harvard University), Ellen Shrock(Harvard University), Benjamin W. Pruitt, Nicholas Conway, Daniel B. Goodman(Harvard University), Cameron L. Gardner(Harvard University), Gary Tyree(Harvard University), Alexandra S. Gonzales(Harvard University), Barry L. Wanner(Harvard University), Julie E. Norville(Harvard University), Marc J. Lajoie(Harvard University), George M. Church(Harvard University)
Science
August 18, 2016
10.1126/science.aaf3639
Cited by 298Open Access
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Abstract

Recoding--the repurposing of genetic codons--is a powerful strategy for enhancing genomes with functions not commonly found in nature. Here, we report computational design, synthesis, and progress toward assembly of a 3.97-megabase, 57-codon Escherichia coli genome in which all 62,214 instances of seven codons were replaced with synonymous alternatives across all protein-coding genes. We have validated 63% of recoded genes by individually testing 55 segments of 50 kilobases each. We observed that 91% of tested essential genes retained functionality with limited fitness effect. We demonstrate identification and correction of lethal design exceptions, only 13 of which were found in 2229 genes. This work underscores the feasibility of rewriting genomes and establishes a framework for large-scale design, assembly, troubleshooting, and phenotypic analysis of synthetic organisms.

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