Art English

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Simplification of the genetic code: diversity restricted genetically encoded amino acids
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ABSTRACT
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In the early stages of the evolution of the universal genetic code, less than 20 aminoacids were considered to be used. Although this notion is supported by a wide range of data, the actual existence and function of the genetic codes with a limited set of canonical amino acids have not been addressed experimentally, in contrast to the successful development of expanded codes. Then artificial genetic code is constructed involving a reduced alphabet. In one of the codes, a variantwith the tRNA anticodon Trp Ala alanine reassigns an unassigned codon UGG system coliS30 Escherichia cell free translation lacking tryptophan. It was confirmed that the efficiency and accuracy of protein synthesis by the code-lacking Trp were comparable to the universal genetic code, by amino acid composition analysis, green fluorescent protein fluorescence measurements and the determination of thecrystal structure . We have also shown that other code, which UGU / UGC codons are assigned to Ser, synthesizes an active enzyme. This method not only provide new insights into primordial genetic codes, but also a tool for engineering proteins essential for evaluation of the early stages of the evolution of proteins and improved pharmaceuticals.
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INTRODUCTION
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The 20 standard amino acid codons are assigned meaning in the universal genetic code. Since this assignment is used by almost all organisms, this code has been regarded as "universal" (1). The genetic code, however, was found tobe pliable, with the discovery of deviant codes (2-4). For example, the CUG codons are assigned to serine (Ser), instead of leucine (Leu), in Candida cylindracea. In laboratory experiments, the researchers were able to expand the genetic code to include unnatural amino acids (5-7). Furthermore, pyrrolysine, which arose from the natural expansion of the genetic code, is incorporated into proteinsin response to UAG nonsense codon (8). These studies demonstrated that the function of protein synthesis codes can be retained even if the mapping between a codon of an amino acid and is different from that in the universal genetic code.
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From an evolutionary standpoint, the genetic code is considered to have evolved from primitive forms containinga limited set of amino acids (1, 9, 10). Chemical evolution experiments indicate that only a limited number of canonical amino acids were available prebiotic environments (11, 12), and therefore the other amino acids which are derived from changes in amino acid biosynthesis (9). Moreover, phylogenies of the aminoacyl-tRNA synthetase (aaRSs) (13) suggest that the genetic codes the amino acids havegained.
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Although no bodies using less than 20 amino acids have been discovered, all known Archaea and some bacteria lacking asparaginyl-tRNA synthetase and / or glutaminyl-tRNA synthetase,and some methanogenic archaea lack cysteinyl synthetase-tRNA. They use 20 amino acids in their genetic codes by a synthesis method in which the first one amino acid is not bound to cognate tRNA, and then the non-cognate amino acid is converted to the cognate tRNA one modifying enzymes dependent (14 -18). These indirect aminoacylation pathways are considered to have been existing routes before...