Expanding The Genetic Code

We worked in many different scientific fields to find suitable ways for the translational incorporate of non-canonical amino acids into proteins. Repurposing existing codons or incorporating new bases are two possible ways. We realized both ways to expand the genetic code of Escherichia coli. The repurposing of a codon for the incorporation of a non-canonical amino acid (ncAA) is possible using the rarely used amber stop codon UAG or other rarely used codons like the leucine codon CUA. To incorporate a non-canonical amino acid using these codons, an orthogonal tRNA/aminoacyl-tRNA synthetase (tRNA/aaRS) pair is necessary, which can charge the ncAA to the tRNA. We designed and synthetized the novel ncAA Nγ‑2‑cyanobenzothiazol‑6‑yl‑L‑asparagine (CBT-asparagine). This ncAA has the chemical ability of perform a highly specific covalent binding reaction, which we wanted to incorporate into our target protein. Therefore, we created a library of aaRS with random mutagenized amino acid binding sites and a selection system to select for the aaRS that specifically incorporates the ncAA. In parallel to the libary and selection based approach, we modeled the aaRS which could incorporate our new amino acid CBT-asparagine. We demonstrated that both ways are suitable for the evolution of aaRS. Although incorporation of ncAAs through the amber codon works, there are challenges associated with this approach. The repurposing of codons leads to the decrease of the growth rate of E. coli and it is only feasible to incorporate up to two different ncAAs. Therefore, we took a new way to incorporate ncAAs. The incorporation of an unnatural base pair into the DNA generates 64 new codons. Our first challenge was the uptake of the unnatural base from the media, because E.coli has no nucleoside triphosphate transporter and is not able to synthetize the bases itself. We cloned a nucleoside triphosphate transporter that enables the uptake of both bases from the media. Furthermore, we analyzed the transcriptome of the plant Croton tiglium, which produces the unnatural base isoG. The transcriptome revealed an enzyme for the biosynthesis, which was cloned and characterized for the biosynthesis of isoG in E. coli. To detect the unnatural base we developed two orthogonal systems. A restriction experiment based on the software tool M.A.X. and an adaption of the Oxford Nanopore sequencing, which were combined into one software suite. To demonstrate the possibilities offered by the incorporation of ncAAs, we developed a toolbox containing five different tools. We chose seven different ncAAs for these five tools and demonstrated interesting applications for them. These ncAAs can be used for various approaches in basic research, medicine and manufacturing. Furthermore, with our submitted parts, every iGEM team can incorporate these ncAAs into their target proteins. Regarding our project, two of the ncAAs that are part of our toolbox perform an autocatalytic reaction upon irradiation with ultraviolet light. Therefore, we decided to build our own LED panel that allows us to perform experiments with these non‑canonical amino acids under reproducible irradiation conditions.