Expanding the Genetic Code

Wang, Lei; Schultz, Peter G.

doi:10.1002/anie.200460627

Cited by 637 publications

(433 citation statements)

References 339 publications

(387 reference statements)

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“…In the case of the genetic code, the adaptor is a charged tRNA, whose anticodon loop recognizes the codon, while the charged stem brings in the cognate amino-acid. It should be possible to change a code without changing the laws of physicochemistry, by designing another adaptor [35]; this is the case for the genetic code, where artificial code variants have been designed by modifying the tRNAs, thus demonstrating the arbitrariness of the code [71].…”

Section: A Biological Code Relies On a Co-evolved Adaptormentioning

confidence: 99%

Chromatin fiber allostery and the epigenetic code

Lesne

Foray

Cathala

et al. 2015

J. Phys.: Condens. Matter

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Abstract. The notion of allostery introduced for proteins about fifty years ago has been extended since then to DNA allostery, where a locally triggered DNA structural transition remotely controls other DNA-binding events. We further extend this notion and propose that chromatin fiber allosteric transitions, induced by histone-tail covalent modifications, may play a key role in transcriptional regulation. We present an integrated scenario articulating allosteric mechanisms at different scales: allosteric transitions of the condensed chromatin fiber induced by histone-tail acetylation modify the mechanical constraints experienced by the embedded DNA, thus possibly controlling DNA-binding of allosteric transcription factors or further allosteric mechanisms at the linker DNA level. At a higher scale, different epigenetic constraints delineate different statistically dominant subsets of accessible chromatin fiber conformations, which each favors the assembly of dedicated regulatory complexes, as detailed on the emblematic example of the mouse Igf2-H19 gene locus and its parental imprinting. This physical view offers a mechanistic and spatially structured explanation of the observed correlation between transcriptional activity and histone modifications. The evolutionary origin of allosteric control supports to speak of an "epigenetic code", by which events involved in transcriptional regulation are encoded in histone modifications in a context-dependent way.

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Section: A Biological Code Relies On a Co-evolved Adaptormentioning

confidence: 99%

Chromatin fiber allostery and the epigenetic code

Lesne

Foray

Cathala

et al. 2015

J. Phys.: Condens. Matter

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“…The discovery of new mutant aaRS activities for global replacement of natural amino acids by noncanonical counterparts can be greatly accelerated by the efficient screening of libraries of mutant aaRS. Such an approach has proved fruitful in generating novel aaRS activity for the related problem of site-specific incorporation of noncanonical amino acids (15,16). Here we describe a rapid, flow-cytometry-based screening protocol to examine libraries of mutant aaRS for their ability to enable incorporation of reactive amino acids into proteins, and we demonstrate its application to the Escherichia coli methionyl-tRNA synthetase (MetRS).…”

mentioning

confidence: 99%

Discovery of aminoacyl-tRNA synthetase activity through cell-surface display of noncanonical amino acids

Link

Vink

Agard

et al. 2006

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

175

154

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The incorporation of noncanonical amino acids into recombinant proteins in Escherichia coli can be facilitated by the introduction of new aminoacyl-tRNA synthetase activity into the expression host. We describe here a screening procedure for the identification of new aminoacyl-tRNA synthetase activity based on the cell surface display of noncanonical amino acids. Screening of a saturation mutagenesis library of the E. coli methionyl-tRNA synthetase (MetRS) led to the discovery of three MetRS mutants capable of incorporating the long-chain amino acid azidonorleucine into recombinant proteins with modest efficiency. The Leu-13 3 Gly (L13G) mutation is found in each of the three MetRS mutants, and the MetRS variant containing this single mutation is highly efficient in producing recombinant proteins that contain azidonorleucine.azide-alkyne ligation ͉ azidohomoalanine ͉ azidonorleucine ͉ click chemistry

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“…However, there does not appear to be an inherent limit to the size or chemical nature of the genetic code, since it has been shown that additional amino acids can be genetically encoded in both prokaryotic and eukaryotic organisms in response to nonsense or frameshift codons (4,5). This requires a unique codon-suppressor tRNA pair and the corresponding aminoacyl-tRNA synthetase, which do not crossreact with the amino acids, tRNAs, or synthetases of the host organism (4,5). The specificity of the aminoacyl tRNA synthetase is then altered by generating large libraries of active-site mutants and passing them through positive and negative selections to identify synthetases that selectively acylate the cognate tRNA with the unnatural amino acid but not any of the common amino acids.…”

mentioning

confidence: 99%

Structural plasticity of an aminoacyl-tRNA synthetase active site

Turner

Graziano

Spraggon

et al. 2006

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

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Recently, tRNA aminoacyl-tRNA synthetase pairs have been evolved that allow one to genetically encode a large array of unnatural amino acids in both prokaryotic and eukaryotic organisms. We have determined the crystal structures of two substrate-bound Methanococcus jannaschii tyrosyl aminoacyl-tRNA synthetases that charge the unnatural amino acids p-bromophenylalanine and 3-(2-naphthyl)alanine (NpAla). A comparison of these structures with the substratebound WT synthetase, as well as a mutant synthetase that charges p-acetylphenylalanine, shows that altered specificity is due to both side-chain and backbone rearrangements within the active site that modify hydrogen bonds and packing interactions with substrate, as well as disrupt the ␣8-helix, which spans the WT active site. The high degree of structural plasticity that is observed in these aminoacyltRNA synthetases is rarely found in other mutant enzymes with altered specificities and provides an explanation for the surprising adaptability of the genetic code to novel amino acids.x-ray crystal structure ͉ unnatural amino acids ͉ expanded genetic code ͉ molecular evolution W ith the rare exceptions of selenocysteine (1) and pyrrolysine (2, 3), the common 20 amino acids are conserved across all known organisms. However, there does not appear to be an inherent limit to the size or chemical nature of the genetic code, since it has been shown that additional amino acids can be genetically encoded in both prokaryotic and eukaryotic organisms in response to nonsense or frameshift codons (4, 5). This requires a unique codon-suppressor tRNA pair and the corresponding aminoacyl-tRNA synthetase, which do not crossreact with the amino acids, tRNAs, or synthetases of the host organism (4, 5). The specificity of the aminoacyl tRNA synthetase is then altered by generating large libraries of active-site mutants and passing them through positive and negative selections to identify synthetases that selectively acylate the cognate tRNA with the unnatural amino acid but not any of the common amino acids. This approach has been used to add Ͼ30 unnatural amino acids to the genetic codes of bacteria, yeast, and mammalian cells with high fidelity and efficiencies.In Escherichia coli, a tyrosyl aminoacyl-tRNA synthetase (TyrRS) tRNA CUA Tyr pair from the archea Methanococcus jannaschii (Mj) was used as an orthogonal tRNA synthetase pair (6). Mutant synthetases have been evolved that selectively aminoacylate their cognate suppressor tRNAs with glycosylated (7), photoreactive (8), and metal-binding amino acids, as well as amino acids with unique functional groups (9-11) . To establish the molecular basis for the surprising adaptability of this synthetase, we solved (12) the structure of a mutant Mj TyrRS that is selective for p-acetylphenylalanine (p-AcPhe). The x-ray crystal structure revealed significant structural changes within the enzyme active site that result from the mutations Y32L, D158G, I159C, and L162R. The Y32L and D158G mutations remove two hydrogen bonds (H-bonds) with the...

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Expanding the Genetic Code

Cited by 637 publications

References 339 publications

Chromatin fiber allostery and the epigenetic code

Chromatin fiber allostery and the epigenetic code

Discovery of aminoacyl-tRNA synthetase activity through cell-surface display of noncanonical amino acids

Structural plasticity of an aminoacyl-tRNA synthetase active site

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