Identification and Evolution of New Orthogonal Aminoacyl-tRNA Synthetase/tRNA Pairs for Genetic Code Expansion

Genetic code expansion is the branch of molecular biology aiming to expand the repertoire of amino acids which can be incorporated into proteins in vivo. A central challenge in expanding the genetic code of cells to incorporate non-canonical amino acids is the scalable discovery of aminoacyl-tRNA synthetase (aaRS)–tRNA pairs (the components of the cellular translational machinery which specify the matching between codons and amino acids) that are orthogonal in their aminoacylation specificity. An orthogonal pair is composed of an aaRS which can interact with its partner tRNA, but not with any other tRNAs in the host, and a tRNA which is substrate to its partner aaRS, but not to any other aaRS in the host. In this research, candidate orthogonal tRNAs were identified from millions of sequences by implementing a computational analysis which scored their likelihood to be recognised by the endogenous aaRSs in E. coli, our model organism. I then developed a rapid, scalable new in vitro approach, named tRNA Extension (tREX), to determine the in vivo aminoacylation status of tRNAs. Using tREX, 243 candidate tRNAs were tested in E. coli and 71 orthogonal tRNAs were identified, covering 16 isoacceptor classes. 23 of those formed functional orthogonal tRNA–cognate aaRS pairs. By performing additional characterisation and molecular evolution of these newly identified functional pairs, we discovered 5 orthogonal pairs, 3 of which displayed high activity in amber suppression, the technique of choice used to implement genetic code expansion in model organisms. I additionally evolved new amino acid substrate specificities for two pairs. Finally, I use tREX to characterize a matrix of 64 orthogonal synthetase-orthogonal tRNA specificities. This work expanded the number of orthogonal pairs available for genetic code expansion, provided a robust pipeline for the discovery of additional orthogonal pairs, and established a foundation for encoding the cellular synthesis of non-canonical biopolymers

Engineering the methanogenic-type seryl-tRNA synthetase from Methanosarcina barkeri: a new methodological approach

Protein synthesis is a fundamental process that involves the transcription of the genetic information contained in the DNA sequence into an mRNA molecule, that will be used as a template for the condensation of amino acids into a polypeptide chain. Such process is guided by the macromolecular complex of the ribosome. Amino acids are delivered to the ribosome linked to an adaptor, a tRNA molecule, capable of base pairing with the mRNA codons, thus coupling the alphabet of DNA with the one of proteins. The fundamental role to link amino acids with the correct tRNAs, generating the decoding scheme, is provided by a class of enzymes known as aminoacyl-tRNA synthetases. Recently, among synthetic biologists the interest grew to expand the genetic code, introducing unnatural amino acids into proteins in vivo engineering the translational apparatus of the cells. If properly chosen, non-canonical amino acids (UAAs) can, for example:mimic or reproduce the effect of post-translational modification on residues of biological interest;selectively label proteins in a non-invasive manner; interfere with proteins' activity with high spatial/temporal resolution etc. For this technology to work, it is essential that a tRNA/synthetase pair exists that does not interfere with the endogenous translational apparatus (namely, that is orthogonal), and that can link the UAA to the tRNA. There are at least two orthogonal tRNA/synthetase pairs for E. coli: the tRNATyr/tyrosyl-tRNA synthetase from Methanocaldococcus jannaschii and the tRNAPyl/pyrrolysyl-tRNA synthetase from Methanosarcina barkeri or mazei, both of which were engineered to recognise several different UAAs. Recently, the tRNASer/seryl-tRNA synthetase from Methanosarcina barkeri was observed to be orthogonal in E. coli and to possess several others properties that make it a suitable candidate to become a new tool for the genetic code expansion. Nevertheless, this possibility has not been explored so far. In this thesis I will describe an attempt to engineer the active site of the enzyme in order to allow the incorporation of different amino acids. To do so, two different libraries of mutants were built using site-saturation mutagenesis and analysed to find mutants active on the desired substrates. While hits of interest were not experimentally observed, possible candidates were found bioinformatically from the data analysis of a high-throughput experiment using NGS and will be tested in the near future. Furthermore, I developed new tools to improve the library construction process and overcome some of the difficulties that I faced during the experimental work

Genetically programmed cell-based synthesis of non-natural peptide and depsipeptide macrocycles.

The direct genetically encoded cell-based synthesis of non-natural peptide and depsipeptide macrocycles is an outstanding challenge. Here we programme the encoded synthesis of 25 diverse non-natural macrocyclic peptides, each containing two non-canonical amino acids, in Syn61Δ3-derived cells; these cells contain a synthetic Escherichia coli genome in which the annotated occurrences of two sense codons and a stop codon, and the cognate transfer RNAs (tRNAs) and release factor that normally decode these codons, have been removed. We further demonstrate that pyrrolysyl-tRNA synthetase/tRNA pairs from distinct classes can be engineered to direct the co-translational incorporation of diverse alpha hydroxy acids, with both aliphatic and aromatic side chains. We define 49 engineered mutually orthogonal pairs that recognize distinct non-canonical amino acids or alpha hydroxy acids and decode distinct codons. Finally, we combine our advances to programme Syn61Δ3-derived cells for the encoded synthesis of 12 diverse non-natural depsipeptide macrocycles, which contain two non-canonical side chains and either one or two ester bonds

Genetically programmed cell-based synthesis of non-natural peptide and depsipeptide macrocycles.

The direct genetically encoded cell-based synthesis of non-natural peptide and depsipeptide macrocycles is an outstanding challenge. Here we programme the encoded synthesis of 25 diverse non-natural macrocyclic peptides, each containing two non-canonical amino acids, in Syn61Δ3-derived cells; these cells contain a synthetic Escherichia coli genome in which the annotated occurrences of two sense codons and a stop codon, and the cognate transfer RNAs (tRNAs) and release factor that normally decode these codons, have been removed. We further demonstrate that pyrrolysyl-tRNA synthetase/tRNA pairs from distinct classes can be engineered to direct the co-translational incorporation of diverse alpha hydroxy acids, with both aliphatic and aromatic side chains. We define 49 engineered mutually orthogonal pairs that recognize distinct non-canonical amino acids or alpha hydroxy acids and decode distinct codons. Finally, we combine our advances to programme Syn61Δ3-derived cells for the encoded synthesis of 12 diverse non-natural depsipeptide macrocycles, which contain two non-canonical side chains and either one or two ester bonds

Adding α,α-disubstituted and β-linked monomers to the genetic code of an organism

Acknowledgements: This work was supported by the Medical Research Council (MRC), UK (MC_U105181009 and MC_UP_A024_1008) and an ERC Advanced Grant SGCR, all to J.W.C. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. D.L.D. was supported by the Boehringer Ingelheim Fonds and Magdalene College, Cambridge. A.D. was supported by the Swiss Study Foundation. The authors thank S. Oehm and Z. Tnimov for useful discussions; W. Schmied for initial discussions on acylation-based synthetase selection; C. Franco, H. Kramer, T. Morgan and F. Begum at the MRC-LMB mass spectrometry facility and K. Heesom at the proteomics facility of the University of Bristol for performing mass spectrometry; and A. Gautam for assistance and support in using the beamline. We acknowledge the European Synchrotron Radiation Facility (ESRF) for provision of synchrotron radiation facilities.The genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1–3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4–6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs—this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-l-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs in Escherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several β-amino acids, α,α-disubstituted-amino acids and β-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of β-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers

Adding α,α-disubstituted and β-linked monomers to the genetic code of an organism

Acknowledgements: This work was supported by the Medical Research Council (MRC), UK (MC_U105181009 and MC_UP_A024_1008) and an ERC Advanced Grant SGCR, all to J.W.C. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. D.L.D. was supported by the Boehringer Ingelheim Fonds and Magdalene College, Cambridge. A.D. was supported by the Swiss Study Foundation. The authors thank S. Oehm and Z. Tnimov for useful discussions; W. Schmied for initial discussions on acylation-based synthetase selection; C. Franco, H. Kramer, T. Morgan and F. Begum at the MRC-LMB mass spectrometry facility and K. Heesom at the proteomics facility of the University of Bristol for performing mass spectrometry; and A. Gautam for assistance and support in using the beamline. We acknowledge the European Synchrotron Radiation Facility (ESRF) for provision of synchrotron radiation facilities.The genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1–3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4–6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs—this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-l-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs in Escherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several β-amino acids, α,α-disubstituted-amino acids and β-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of β-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers

Adding α,α-disubstituted and β-linked monomers to the genetic code of an organism.

Acknowledgements: This work was supported by the Medical Research Council (MRC), UK (MC_U105181009 and MC_UP_A024_1008) and an ERC Advanced Grant SGCR, all to J.W.C. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. D.L.D. was supported by the Boehringer Ingelheim Fonds and Magdalene College, Cambridge. A.D. was supported by the Swiss Study Foundation. The authors thank S. Oehm and Z. Tnimov for useful discussions; W. Schmied for initial discussions on acylation-based synthetase selection; C. Franco, H. Kramer, T. Morgan and F. Begum at the MRC-LMB mass spectrometry facility and K. Heesom at the proteomics facility of the University of Bristol for performing mass spectrometry; and A. Gautam for assistance and support in using the beamline. We acknowledge the European Synchrotron Radiation Facility (ESRF) for provision of synchrotron radiation facilities.The genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1-3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4-6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs-this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-L-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs in Escherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several β-amino acids, α,α-disubstituted-amino acids and β-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of β-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers