This work proves that life tolerates radical compression of its genetic code—reducing 64 to 57 codons genome-wide—freeing multiple codon slots to encode non-canonical amino acids and redefining the boundaries of synthetic biology.
A viable Escherichia coli strain with a synthetic 4 Mb genome encoding a 57-codon genetic code can be created through systematic genome-wide recoding of over 100,000 codons, achieved by combining empirically validated codon compression schemes with iterative defect mapping and targeted fixing strategies that overcome initial design failures across all genomic regions.
The near-universal genetic code of living organisms uses 64 codons to encode the 20 canonical amino acids in protein synthesis. Here we design and generate a variant of Escherichia coli with a 4 Mb synthetic genome in which we replace every known occurrence of six sense codons and a stop codon with synonymous codons. We thereby recode 105 codons to create an organism with a 57-codon genetic code; this organism – which we name Syn57 – uses 55 codons to encode the 20 canonical amino acids.