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Science. 2016 Aug 19;353(6301):819-22. doi: 10.1126/science.aaf3639.

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

Author information

1
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
2
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Program in Systems Biology, Harvard University, Cambridge, MA 02138, USA. Ecole des Mines de Paris, Mines Paristech, Paris 75272, France.
3
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA.
4
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Program in Biophysics, Harvard University, Boston, MA 02115, USA.
5
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
6
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
7
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02138, USA.
8
Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA.
9
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
10
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. mlajoie@uw.edu gchurch@genetics.med.harvard.edu.
11
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA. mlajoie@uw.edu gchurch@genetics.med.harvard.edu.

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.

PMID:
27540174
DOI:
10.1126/science.aaf3639
[Indexed for MEDLINE]
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