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Figure 3 | Biology Direct

Figure 3

From: One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation

Figure 3

Risk of confusion of complementary anticodons (at the purine/pyrimidine R/Y resolution) under four scenarios of tRNA recognition by two putative r-aaRSs (adopted from [12]). Pairs of complementary anticodons are ordered following the "yin-yang" pattern of Figure 1B. Plus signs denote the pairs that have no identical tetra(or more)- nucleotides within the loop 3' YU-XYZ-RN5' --- that is, they are distinguishable (under the corresponding scenario) by two putative ribozymes that recognize the complementary tRNA halves. Minus signs mark the contrary, indistinguishable, cases. For each pair, only a zero- or one base-long shift in one of two directions from the anticodon is allowed. Two simultaneous shifts (one in each anticodon loop) are considered highly unlikely. All 32 pairs are divided in four quarters (enumerated I, II, III, and IV) according to the sub-code for two complementary modes of tRNA aminoacylation. The earliest quarter is supposed to be I, the latest, IV (see text for detail). The quarters II and III include 16 RY vs. YR-type pairs that satisfy the second rule of the subcode for two aminoacylations (see legend to Figure 1B). If, following Figure 4, we assign NGN and NAN anticodons to major and minor groove sides, this would exclude the entire 3' × 5' scenario (shaded) and the number of conceivable scenarios of tRNA recognition is reduced from four to only two (enclosed by rectangles). The actual evolutionary pathway is shown in green.

a5'ANN3' anticodons usually do not exist – instead, the 5'GNN3' anticodons recognize not only the legitimate 3'CИИ5' codons but also the illegitimate wobbling 3'UИИ5' codons. For the strictly legitimate nine pairs of the RY vs. YR type, the +/- ratio is 7:2 (second scenario) vs. 3:6 (fourth scenario) – the former being, therefore, seven times more "secure".

Pairs of pentanucleotides 5'U-XYZ-R3' on the right (with complementary anticodons in the center) show the risk of confusion by r-aaRSs under the 5' × 3' scenario of recognition for the corresponding pairs from quarters I, II, III and IV. Compare the risk of confusion for I vs. IV and II vs. III (see text for detail).

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