One challenge for synthetic biologists is the predictable tuning of genetic circuit regulatory components to elicit desired outputs. Gene expression driven by ligand-inducible transcription factor systems must exhibit the correct ON and OFF characteristics: appropriate activation and leakiness in the presence and absence of inducer, respectively. However, the dynamic range of a promoter (i.e., absolute difference between ON and OFF states) is difficult to control. We report a method that tunes the dynamic range of ligand-inducible promoters to achieve desired ON and OFF characteristics. We build combinatorial sets of AraC-and LasR-regulated promoters containing −10 and −35 sites from synthetic and Escherichia coli promoters. Four sequence combinations with diverse dynamic ranges were chosen to build multi-input transcriptional logic gates regulated by two and three ligand-inducible transcription factors (LacI, TetR, AraC, XylS, RhlR, LasR, and LuxR). This work enables predictable control over the dynamic range of regulatory components.

Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion with non-canonical amino acids, yet understanding of its structure and activity is incomplete. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNAPyl. This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNAPyl recognition by PylRS is anticodon-independent; the anticodon does not contact the enzyme. Using standard microbiological culture equipment, we then established a new method for laboratory evolution – a non-continuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. We finally employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a non-canonical amino acid.

Selenocysteine (Sec) is naturally incorporated into proteins by recoding the stop codon UGA. Sec is not hardwired to UGA, as we found the Sec insertion machinery to be able to site-specifically incorporate Sec directed by 58 of the 64 codons. For 15 sense codons, complete conversion of the codon meaning from canonical amino acid to Sec was observed along with a 10-fold increase in selenoprotein yield compared to Sec insertion at the three stop codons. This high-fidelity sense-codon recoding mechanism was demonstrated for Escherichia coli formate dehydrogenase and recombinant human thioredoxin reductase and confirmed by independent biochemical and biophysical methods. Although Sec insertion at UGA is known to compete against protein termination, it is surprising that the Sec machinery has the ability to outcompete abundant aminoacyl-tRNAs in decoding sense codons. The findings have implications for the process of translation and the information storage capacity of the biological cell.

Selenocysteine (Sec) biosynthesis in archaea and eukaryotes requires three steps: serylation of tRNASec by seryl-tRNA synthetase (SerRS), phosphorylation of Ser-tRNASec by O-phosphoseryl-tRNASec kinase (PSTK), and conversion of O-phosphoseryl-tRNASec (Sep-tRNASec) by Sep-tRNA:Sec-tRNA synthase (SepSecS) to Sec-tRNASec. Although SerRS recognizes both tRNASec and tRNASer species, PSTK must discriminate Ser-tRNASec from Ser-tRNASer. Based on a comparison of the sequences and secondary structures of archaeal tRNASec and tRNASer, we introduced mutations into Methanococcus maripaludis tRNASec to investigate how Methanocaldococcus jannaschii PSTK distinguishes tRNASec from tRNASer. Unlike eukaryotic PSTK, the archaeal enzyme was found to recognize the acceptor stem rather than the length and secondary structure of the D-stem. While the D-arm and T-loop provide minor identity elements, the acceptor stem base pairs G2-C71 and C3-G70 in tRNASec were crucial for discrimination from tRNASer. Furthermore, the A5-U68 base pair in tRNASer has some antideterminant properties for PSTK. Transplantation of these identity elements into the tRNASerUGA scaffold resulted in phosphorylation of the chimeric Ser-tRNA. The chimera was able to stimulate the ATPase activity of PSTK albeit at a lower level than tRNASec, whereas tRNASer did not. Additionally, the seryl moiety of Ser-tRNASec is not required for enzyme recognition, as PSTK efficiently phosphorylated Thr-tRNASec.

We tested the substrate range of four wild-type Escherichia coli aminoacyl-tRNA synthetases (AARSs) with a library of non-standard amino acids (nsAAs). While these AARSs could discriminate efficiently against the other canonical amino acids, they were able to use many nsAAs as substrates. Our results also showed E. coli tryptophanyl-tRNA synthetase (TrpRS) and tyrosyl-tRNA synthetase to have overlapping substrate ranges. In addition, we found that the nature of the anticodon sequence of tRNATrp altered the nsAA substrate range of TrpRS; this implies that the sequence of the anticodon affects the TrpRS amino acid binding pocket. These results highlight again that inherent AARS polyspecificity will be a major challenge to the goal of incorporating multiple different amino acids site-specifically into proteins.