> I wonder if they just got lucky with (or perhaps strategically chose) the specific codon substitutions to perform? Would a different set of synonym substitutions have been nonviable?
Recoding scheme was strategically chosen. They cite 2016 paper (PMC5035903) which showed substituting AGA with CGA (synonymous codon for arginine) on E. coli was nonviable.
> Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multidimensional “safe replacement zone” (SRZ) within which alternative codons are more likely to be viable.
Recoding scheme was strategically chosen. They cite 2016 paper (PMC5035903) which showed substituting AGA with CGA (synonymous codon for arginine) on E. coli was nonviable.