Anticodon discrimination base

Another hypothesis was provided by Mikio Shimitso (1982) on the basis of studies of steric effects in molecular models. It had been noted years previously that the fourth nucleotide at the 3 end of the tRNA molecules (referred to as the discrimination base) might have a recognition function. In the case of certain amino acids (i.e., their tRNA-amino acid complexes) this base pair, in combination with the anticodon of the tRNA molecule, can select the amino acid corresponding to the tRNA species in question this is done on the basis of the stereochemical properties of the molecule. Since the anticodon of a tRNA molecule and the fourth nucleotide of the acceptor stem are far apart in space, two tRNA molecules must complex in a head-to-tail manner. The pocket thus formed can then fit specifically to the corresponding amino acid. 

One important question is that of the order in which the basic mechanisms of evolution processes, leading eventually to the emergence of life, occurred. As far as the development of the genetic code is concerned, it is not clear whether the code evolved prior to the aminoacylation process, i.e., whether aminoacyl-tRNA synthetases evolved before or after the code. A tRNA species which is aminoacy-lated by two different synthetases was studied if this tRNA had important identity elements such as the discriminator base and the three anticodon bases for the two synthetases, this would be evidence that the aminoacyl-tRNA synthetases had developed after the genetic code. Dieter Soil s group, which is experienced in working with this family of enzymes, came to the conclusion that the universal genetic code must have developed before the evolution of the aminoacylation system (Hohn et al, 2006). 

The first orthogonal E. coli tRNA-synthetase pair generated from archaeal bacteria was derived from the tyrosyl pair taken from Methanococcus janmschii In vitro experiments showed that the major recognition elements of M. jannaschii tRNA" include the discriminator base A73 and the first base pair, C1-G72, in the acceptor stem (Figure 2(a)). The anticodon triplet participates only weakly in identity determination. By contrast, E. coli uses A73, G1-C72, a long variable arm, and the anticodon as identity elements. The M. 

Most identity elements are present at the two distal ends of the molecule the acceptor stem and the triplet anticodon (Fig. 5). In the acceptor stem, the unpaired discriminator base N73 is a crucial recognition factor for most aaRSs. Also, the first few acceptor stem base pairs often serve as determinants for many tRNAs. The structural domains of aaRSs play specific roles in the recognition of tRNAs (12). In general, the more conserved catalytic domain binds the acceptor stem during aminoacylation. As indicated, diverged domains in most aaRSs interact directly... 

Depending on the tRNA species, the interaction of tRNAs with their cognate aminoacyl-tRNA synthetases involves varying degrees of contacts over the surface of the two macromolecules (196). The structural elements of tRNA responsible for defining the amino acid acceptor specificity are called identity elements or discriminator bases. Among the major identity elements are the amino acid acceptor stem and the anticodon. 

Discrimination between some pairs of tRNAs depends entirely on the anticodon sequence. For example, tRNAMet contains the anticodon CAU. That for a minor tRNAIle is the same except that the cytosine has been posttranscriptionally modified by covalent linkage of a molecule of lysine via its e-amino group to C2 of the cytosine. The latter base (Iysidine) is correctly recognized by E. coli isoleucyl-tRNA synthetase but, if the cytosine is unmodified, it is aminoacylated by methionyl-tRNA synthetase.192 In most instances the acceptor specificity, or tRNA identity, is not determined solely by the anticodon sequence. Thus, when a methionine initiator tRNA was modified to contain a tryptophan anticodon, it was only partially charged with tryptophan in vivo. However, when A73 of the methionine tRNA was also converted to G73, only tryptophan was inserted.193 Nucleotide 73 (Fig. 

For tRNA and tRNA % the anticodon and other parts of the tRNAs are dispensable for aminoacylation, while the acceptor stem sequences with the 7-bp helix containing G3 U70 (in tRNA ) serve as the only sufficient discriminator (201). The conserved G3 -U70 base pair in tRNA is a major determinant in... 

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