The Tryptophan-Induced tnaC Ribosome Stalling Sequence Exposes High Amino Acid Cross-Talk That Can be Mitigated By Removal of NusB for Higher Orthogonality

A growing number of engineered synthetic circuits have employed biological parts coupling transcription and translation in bacterial systems to control downstream gene expression. One example, the leader sequence of the tryptophanase (tna) operon, is a commonly employed L-tryptophan inducible circuit controlled by ribosome stalling. While induction of the tna operon has been well-characterized in response to L-tryptophan, cross-talk of this modular component with other metabolites in the cell, such as other naturally-occurring amino acids, have been less explored. In this study, we investigated the impact of natural metabolites and E. coli host factors on induction of the tna leader sequence. To do so, we constructed and biochemically validated an experimental assay using the tna operon leader sequence to assess differential regulation of transcription elongation and translation in response to L-tryptophan. Operon induction was then assessed following addition of each of the 20 naturally-occurring amino acids to discover that several additional amino acids (e.g. L-alanine, L-cysteine, L-glycine, L-methionine, and L-threonine) also induce expression of the tna leader sequence. Following characterization of dose-dependent induction by L-cysteine relative to L-tryptophan, the effect on induction by single gene knockouts of protein factors associated with transcription and/or translation were interrogated. Our results implicate the endogenous cellular protein, NusB, as an important factor associated with induction of the operon by the alternative amino acids. As such, removal of the nusB gene from strains intended for tryptophan-sensing utilizing the tna leader region reduces amino acid cross-talk, resulting in enhanced orthogonal control of this commonly used synthetic system.