Figure 2.

Shown are the schematic modes of original tRNA–aaRS recognition with the single-stranded anticodon derived either from the 5′ strand (A) or the 3′ strand (B) of the primordial palindromic acceptor (6). The latter is presented in the center with the second base pair in boldface. The two types of proto-aaRSs are drawn as approaching the acceptor from the opposite sides, in accordance with the complementarity of the head-to-tail aligned signature motifs of aaRSs from the two classes, remarkably just within their catalytic domains (6, 10). In turn, each of the two proto-aaRSs is subdivided into two groups (I₁, I₂ and symmetrically II₂, II₁) depending on the second base pair, C2-G71 or G2-C71, respectively. For each amino acid, the corresponding third base of the acceptor and 73rd base-determinator are shown in brackets; the G3 for ALA bears an asterisk since the opposite “wobbling” U70 base strongly determines the identity of tRNA^Ala (2, 3). tRNA^His is also marked as a unique tRNA with the paired base-determinator, G-1:G73. Some of amino acids are marked by α or β in accordance with either α-helical or β-barrel structure of the aaRS anticodon-binding domain. Italicized are tRNAs for Cys and Trp with ambiguous consensus “S” at the acceptor second position symbolizing either C or G (Table 2); accordingly their anticodons could originate from 5′ or 3′ strand. In bold are shown the amino acids whose anticodons have the same second base as in the acceptor. Four of them, GLY, ALA, PRO (class II), and ARG (class I), are shown in boldfaced capital as they are presumably the first ones recruited in translation. Note that tRNAs for all the four “early” amino acids have the anticodon of the 5′ strand origin (A). In normal type are shown the amino acids with a changed central base in the anticodon caused by C → U or G → A transitions. Two-sided arrows connect tRNAs with complementary anticodons. In A, most such tRNAs are aminoacylated by complementary aaRSs—i.e., I₁ × II₁ and I₂ × II₂. Contrarily, in B, all complementarily connected amino acids except Arg have been involved later in translation. Again a majority of these are activated by aaRSs of the same class—i.e., I₁ × I₂ and II₁ × II₂. N = {G,C,A,U}, B = {G,C,U}, R = {G,A}, Y = {C,U}, K = {G,U}, M = {A,C}, S = {G,C}, W = {A,U}.