Systematic Synonymous Codon Compression Demonstrates Genome-Scale Codon Removal Is Viable in E. coli

Published in Nature in 2016, this paper established the foundational scientific principle behind Constructive Bio's platform: that synonymous codons can be progressively removed from the E. coli genome at large scale while maintaining a viable, functional organism.

The genetic code is redundant. Most amino acids are encoded by multiple synonymous codons, all of which specify the same amino acid during translation. This paper asked whether an organism can tolerate the systematic removal of specific synonymous codons, replacing them genome-wide with alternatives that encode the same protein sequences. If so, the removed codons would become available for reassignment to new functions, including the incorporation of non-canonical amino acids.

The team demonstrated genome-scale codon compression in E. coli, replacing target codons with their synonymous equivalents across large genomic regions. They showed that the organism tolerated these changes, maintaining growth and core cellular functions despite the progressive removal of codons from active use. This was not a foregone conclusion: codon usage in bacteria is under selection pressure, and synonymous codons are not functionally identical in terms of translation speed, mRNA structure, and gene regulation.

This work established the design rules for the much larger-scale recoding projects that followed. Syn61, published in Nature in 2019, applied these principles to the entire 4-million-base-pair E. coli genome, removing three codons completely. Syn57, published in Science in 2025, extended the approach to seven codons. In each case, the viability of genome-scale codon compression was first demonstrated in this 2016 paper.

For Constructive Bio, this publication represents the earliest proof that the core platform concept is scientifically sound: the genetic code of a living organism can be systematically rewritten to create space for new chemistry, without destroying the organism's ability to function as a manufacturing host.