Figure 1

The subcode for two modes of tRNA recognition by aaRSs. (A) The conventional representation of the genetic code table with yellow and blue colors marking two modes of tRNA recognition by aaRSs – from the minor and major groove sides of the acceptor stem, respectively. Lys is colored in lighter shade of blue in order to indicate the fact that some archaebacteria use class I synthetases for this amino acid [9]. Stop codons are colored in yellow because the known cases of their "capture" by amino acids are mostly from class I [8]. Codons AGG and AGA are assigned to blue Ser or Gly, as they are in mitochondria (ibid.) Three aromatic amino acids, Phe, Tyr and Trp, with their mode of tRNA aminoacylation contradicting the class aaRS membership, are italicized. (B) The condensed rearranged table of the genetic code, in which complementary codons are put next to each other (all 32 pairs of complementary anticodons are shown in Figure 3). This rearrangement reveals the following rules of tRNA aminoacylation: (1) If the complementary codons contain YY vs. RR at the second and adjacent (either first or third) positions, their aaRSs recognize the tRNA acceptor from the same side of the groove, namely: minor (yellow) for 5'ИAR3' – 5'YUN3' pairs, or major (blue) for 5'RGИ3' – 5'NCY3' pairs; (2) If these positions are occupied by RY and YR, the modes of tRNA recognition are different, namely: minor (yellow) 5'YGИ3' vs. major (blue) 5'NCR3' and major (blue) 5'ИAY3' vs. minor (yellow) 5'RUN3'. These rules comprise the sub-code for two modes of tRNA aminoacylation that reveal four different quarters of complementary codons denoted by I, II, III and IV. Other symbols: N and complementary И denote all four nucleotides; R, purine (G or A); Y, pyrimidine (C or U). For details, see [11, 12].