Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion

Kobayashi, T.; Nureki, Osamu; Ishitani, R.; Yaremchuk, A.; Tukalo, M. A.; Cusack, Stephen; Sakamoto, K.; Yokoyama, S.

doi:10.2142/biophys.43.s94_1

Cited by 27 publications

(54 citation statements)

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“…Indeed, some experimental work shows the coevolution of tRNAs with their corresponding aminoacyl tRNA synthetases' genes (Salazar et al 2003), and there is room for more such research. In the context of previous works showing the limitation in amino acid ligation when using tRNAs from species of different domains (Ripmaster et al 1995;Kobayashi et al 2003;Namgoong et al 2007;Shaul et al 2010), our results may suggest the existence of informative tRNA positions and code which are species-specific, across all the three domains of life. Our method of analysis for searching potential determinants of selective tRNA aminoacylation could be implemented for other species/kingdoms and may further direct relevant experimental research.…”

Section: Discussionsupporting

confidence: 67%

“…In particular, it is expected that the positions and nucleotides used for recognition of tRNAs by their cognate aminoacyl-tRNA synthetases ("determinants") may vary between distant kingdoms (e.g., species from Archaea vs. Bacteria). Indeed, it has been experimentally shown that a tRNA synthetase from one domain of life will often, but not always (Xu et al 2001), fail to aminoacylate tRNAs from other domains (Ripmaster et al 1995;Kobayashi et al 2003;Namgoong et al 2007). Other studies showed that the aminoacylation specificity of some tRNA types, among distant species, may be determined by the very same base pair in their acceptor stem.…”

Section: Introductionmentioning

confidence: 99%

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Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon

Galili

Gingold

Shaul

et al. 2016

RNA

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Proper recognition of tRNAs by their aminoacyl-tRNA synthetase is essential for translation accuracy. Following evidence that the enzymes can recognize the correct tRNA even when anticodon information is masked, we search for additional nucleotide positions within the tRNA molecule that potentially contain information for amino acid identification. Analyzing 3936 sequences of tRNA genes from 86 archaeal species, we show that the tRNAs' cognate amino acids can be identified by the information embedded in the tRNAs' nucleotide positions without relying on the anticodon information. We present a small set of six to 10 informative positions along the tRNA, which allow for amino acid identification accuracy of 90.6% to 97.4%, respectively. We inspected tRNAs for each of the 20 amino acid types for such informative positions and found that tRNA genes for some amino acids are distinguishable from others by as few as one or two positions. The informative nucleotide positions are in agreement with nucleotide positions that were experimentally shown to affect the loaded amino acid identity. Interestingly, the knowledge gained from the tRNA genes of one archaeal phylum does not extrapolate well to another phylum. Furthermore, each species has a unique ensemble of nucleotides in the informative tRNA positions, and the similarity between the sets of positions of two distinct species reflects their evolutionary distance. Hence, we term this set of informative positions a "tRNA cipher." It is tempting to suggest that the diverging code identified here might also serve the aminoacyl tRNA synthetase in the task of tRNA recognition.

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Section: Discussionsupporting

confidence: 67%

Section: Introductionmentioning

confidence: 99%

Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon

Galili

Gingold

Shaul

et al. 2016

RNA

View full text Add to dashboard Cite

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“…Mutations in the anticodon-binding pocket of aaRSs previously have been shown to improve interactions with nonsense or frameshift suppressor tRNAs (22)(23)(24). These examples suggest that it may be possible to evolve the anticodon-binding pocket of PhProRS to recognize and charge Af-tRNA CUA Pro efficiently.…”

Section: Resultsmentioning

confidence: 97%

Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in Escherichia coli

Chatterjee

Xiao

Schultz

2012

Proc. Natl. Acad. Sci. U.S.A.

101

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The site-specific incorporation of unnatural amino acids (UAAs) into proteins in living cells relies on an engineered tRNA/aminoacyl-tRNA synthetase (tRNA/aaRS) pair, orthogonal to the host cell, to deliver the UAA of choice in response to a unique nonsense or frameshift codon. Here we report the generation of mutually orthogonal prolyl-tRNA/prolyl-tRNA synthase (ProRS) pairs derived from an archaebacterial ancestor for use in Escherichia coli . By reprogramming the anticodon-binding pocket of Pyrococcus horikoshii ProRS (PhProRS), we were able to identify synthetase variants that recognize engineered Archaeoglobus fulgidus prolyl-tRNAs (Af-tRNA Pro ) with three different anticodons: CUA, AGGG, and CUAG. Several of these evolved PhProRSs show specificity toward a particular anticodon variant of Af-tRNA Pro , whereas others are promiscuous. Further evolution of the Af-tRNA Pro led to a variant exhibiting significantly improved amber suppression efficiency. Availability of a prolyl-tRNA/aaRS pair should enable site-specific incorporation of proline analogs and other N-modified UAAs into proteins in E. coli . The evolution of mutually orthogonal prolyl-tRNA/ProRS pairs demonstrates the plasticity of the tRNA–aaRS interface and should facilitate the incorporation of multiple, distinct UAAs into proteins.

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“…When the acyl enzyme is formed, the second aa-tRNA binds with its aminoacyl moiety accommodated in the P2 pocket and its tRNA moiety interacting with residues of the a6-a7 loop. In both TyrRS and TrpRS, the loop equivalent to this a6-a7 loop is involved in tRNA binding 8,[22][23][24] . CDPSs may have retained This study indicates that compared with class-Ic aaRSs, CDPSs have acquired both new active site residues and a new aminoacylbinding site for a second aa-tRNA substrate.…”

Section: Discussionmentioning

confidence: 99%

“…These enzymes possess a common architecture very similar to the catalytic domains of class-I aa-tRNA synthetases (aaRSs), especially class-Ic TyrRSs and TrpRSs. In particular, the aminoacyl moiety of the first aa-tRNA substrate of CDPS is thought to bind in a pocket [4][5][6][7] , structurally corresponding to the tyrosine-binding pocket in TyrRSs (PDB 1J1U 8 ). Accordingly, buffer components were identified within this pocket in several CDPS crystal structures 4,6 .…”

mentioning

confidence: 99%

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases

et al. 2014

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Cyclodipeptide synthases form cyclodipeptides from two aminoacyl transfer RNAs. They use a ping-pong mechanism that begins with transfer of the aminoacyl moiety of the first aminoacyl tRNA onto a conserved serine, yielding an aminoacyl enzyme. Combining X-ray crystallography, site-directed mutagenesis and affinity labelling of the cyclodipeptide synthase AlbC, we demonstrate that the covalent intermediate reacts with the aminoacyl moiety of the second aminoacyl tRNA, forming a dipeptidyl enzyme, and identify the aminoacyl-binding sites of the aminoacyl tRNAs.

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Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion

Cited by 27 publications

References 0 publications

Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon

Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon

Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in Escherichia coli

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases

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