tRNA engineering for manipulating genetic code

Katoh, Takayuki; Iwane, Yoshihiko; Suga, Hiroaki

doi:10.1080/15476286.2017.1343227

Cited by 21 publications

(25 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This “unique participant” model of tRNA function places important restrictions on the choice of tRNAs suitable for the efficient introduction of Uaas into proteins, especially when multiple insertions are desired. Additional reviews of this topic have recently appeared [1,2].…”

Section: Introductionmentioning

confidence: 99%

Evolutionary tuning impacts the design of bacterial tRNAs for the incorporation of unnatural amino acids by ribosomes

Uhlenbeck

Schrader

2018

Current Opinion in Chemical Biology

View full text Add to dashboard Cite

In order to function on the ribosome with uniform rate and adequate accuracy, each bacterial tRNA has evolved to have a characteristic sequence and set of modifications that compensate for the differing physical properties of its esterified amino acid and its codon-anticodon interaction. The sequence of the T-stem of each tRNA compensates for the differential effect of the esterified amino acid on the binding and release of EF-Tu during decoding. The sequence and modifications in the anticodon loop and core of tRNA impact the codon-anticodon strength and the ability of the tRNA to bend during codon recognition. These discoveries impact the design of tRNAs for the efficient and accurate incorporation of unnatural amino acids into proteins using bacterial translation systems.

show abstract

Section: Introductionmentioning

confidence: 99%

Evolutionary tuning impacts the design of bacterial tRNAs for the incorporation of unnatural amino acids by ribosomes

Uhlenbeck

Schrader

2018

Current Opinion in Chemical Biology

View full text Add to dashboard Cite

show abstract

“…A rapidly developing area-the orthogonal translation-also employs a tRNA-suppression strategy to refactor stop codons and incorporate noncanonical amino acids to expand genetic code with new functionalities (reviewed in refs. [49][50][51] ). Here, the amino acid substrates are unnatural, thus repurposing of the tRNA requires a more complex strategy involving modification of the Fig.…”

Section: Discussionmentioning

confidence: 99%

Repurposing tRNAs for nonsense suppression

et al. 2021

View full text Add to dashboard Cite

Three stop codons (UAA, UAG and UGA) terminate protein synthesis and are almost exclusively recognized by release factors. Here, we design de novo transfer RNAs (tRNAs) that efficiently decode UGA stop codons in Escherichia coli. The tRNA designs harness various functionally conserved aspects of sense-codon decoding tRNAs. Optimization within the TΨC-stem to stabilize binding to the elongation factor, displays the most potent effect in enhancing suppression activity. We determine the structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon in the A site at 2.9 Å resolution. In the context of the suppressor tRNA, the conformation of the UGA codon resembles that of a sense-codon rather than when canonical translation termination release factors are bound, suggesting conformational flexibility of the stop codons dependent on the nature of the A-site ligand. The systematic analysis, combined with structural insights, provides a rationale for targeted repurposing of tRNAs to correct devastating nonsense mutations that introduce a premature stop codon.

show abstract

“…These specifically designed ribozymes are able to recognize a large variety of amino acids with an activated carboxyl group and transfer them efficiently to the 3′ end of the tRNAs (Figure 3A). The promiscuous behavior of the flexizymes towards amino acids and tRNAs allows the extensive reprogramming of the genetic code (Figure 3B) [45,46]. By joining the flexible IVT system (such as PURE) with both tRNAs carrying a wide diversity of amino acids charged by flexizymes and the mRNA display technology, the so-called “Random Peptide Integrated Discovery” (RaPID) system was created [3,47].…”

Section: Peptide Discovery Platformmentioning

confidence: 99%

Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery

et al. 2019

View full text Add to dashboard Cite

The scope of targets investigated in pharmaceutical research is continuously moving into uncharted territory. Consequently, finding suitable chemical matter with current compound collections is proving increasingly difficult. Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets. These binders facilitate drug discovery projects both as tools for target validation, structural elucidation and assay development as well as starting points for medicinal chemistry. Novartis internalized two complementing encoded library platforms to accelerate the initiation of its drug discovery programs. For the identification of low-molecular weight ligands, we apply DNA-encoded libraries. In addition, encoded peptide libraries are employed to identify cyclic peptides. This review discusses how we apply these two platforms in our research and why we consider it beneficial to run both pipelines in-house.

show abstract

tRNA engineering for manipulating genetic code

Cited by 21 publications

References 47 publications

Evolutionary tuning impacts the design of bacterial tRNAs for the incorporation of unnatural amino acids by ribosomes

Evolutionary tuning impacts the design of bacterial tRNAs for the incorporation of unnatural amino acids by ribosomes

Repurposing tRNAs for nonsense suppression

Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery

Contact Info

Product

Resources

About