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

Nili Ostrov; Matthieu Landon; Marc Guell; Gleb Kuznetsov; Jun Teramoto; Natalie Cervantes; Minerva Zhou; Kerry Singh; Michael G Napolitano; Mark Moosburner; Ellen Shrock; Benjamin W Pruitt; Nicholas Conway; Daniel B Goodman; Cameron L Gardner; Gary Tyree; Alexandra Gonzales; Barry L Wanner; Julie E Norville; Marc J Lajoie; George M Church

doi:10.1126/science.aaf3639

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

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

Authors

Nili Ostrov¹, Matthieu Landon², Marc Guell³, Gleb Kuznetsov⁴, Jun Teramoto⁵, Natalie Cervantes¹, Minerva Zhou⁶, Kerry Singh⁶, Michael G Napolitano⁷, Mark Moosburner¹, Ellen Shrock¹, Benjamin W Pruitt⁸, Nicholas Conway⁸, Daniel B Goodman³, Cameron L Gardner¹, Gary Tyree¹, Alexandra Gonzales¹, Barry L Wanner⁹, Julie E Norville¹, Marc J Lajoie¹⁰, George M Church¹¹

Affiliations

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.

PMID: 27540174
DOI: 10.1126/science.aaf3639

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Escherichia coli / genetics*
Escherichia coli Proteins / genetics*
Genes, Essential
Genes, Lethal
Genes, Synthetic*
Genetic Code / genetics
Genetic Code / physiology*
Genetic Engineering
Genome, Bacterial*
Phenotype
Protein Biosynthesis / genetics

Substances

Escherichia coli Proteins

Grants and funding

T32 GM008313/GM/NIGMS NIH HHS/United States