Total synthesis of Escherichia coli with a recoded genome

• Published in: Nature (London) Vol. 569; no. 7757; pp. 514 - 518
• Main Authors: Fredens, Julius, Wang, Kaihang, de la Torre, Daniel, Funke, Louise F H, Robertson, Wesley E, Christova, Yonka, Chia, Tiongsun, Schmied, Wolfgang H, Dunkelmann, Daniel L, Beránek, Václav, Uttamapinant, Chayasith, Llamazares, Andres Gonzalez, Elliott, Thomas S, Chin, Jason W
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 01.05.2019
• Subjects: Amino acids; Amino Acids - genetics; Artificial chromosomes; Bacteria; Biosynthesis; Cell Engineering - methods; Chemical synthesis; Codon, Terminator - genetics; Codons; Deoxyribonucleic acid; Design; DNA; E coli; Escherichia coli; Escherichia coli - genetics; Escherichia coli - growth & development; Escherichia coli - metabolism; Gene expression; Genes, Essential - genetics; Genetic aspects; Genetic Code - genetics; Genetic engineering; Genetically modified organisms; Genome, Bacterial - genetics; Genomes; Genomics; Observations; Organic compound synthesis; Proteins; Ribonucleic acid; Ribosomal DNA; RNA; RNA, Transfer - genetics; Science; Stop codon; Synthesis; Synthetic Biology - methods; Transfer RNA
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-019-1192-5

Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon-out of up to 6 synonyms-to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme-with simple corrections at just seven positions-to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.