pCODE tRNA Expression Plasmids Compensate for Rare Codons in Recombinant Protein Production

The molecular mechanisms that constrain recombinant protein production and the importance of synonymous codon usage have not been fully elucidated. Codon frequency varies between different organisms, and rare codons are often avoided in "codon-optimized" synthetic gene constructs. Overexpression of tRNA genes is an alternative strategy to compensate for suboptimal codon usage, but the consequences and limitations of this approach have not been widely studied. Here, we develop and characterize a versatile collection of pCODE plasmids for tRNA overexpression in Escherichia coli and show that they complement rare codons with very modest limitations or negative effects, regardless of the position, type, number, or distribution of rare codons in the expressed gene. One pCODE plasmid encodes an inducible tRNA expression cassette and shows potential as a new type of genetic regulation based on inducible rare codon complementation. The pCODE tRNA expression plasmids provide mechanistic insights into synonymous codon usage and add to the molecular biology toolbox that enables recombinant protein production.