Distribution of family-specific sequence homologies in six families of isoaccepting tRNAs

The nucleotide occupancy of 288 sequences of tRNA has been analyzed for every position on the standard tRnA sequence, except for the anticodon and the variable regions of the D and V loops. Modified nucleotides were assimilated to the canonical nucleotide from which they derive. A X2 test applied at the P = 0.01 level of significance showed family-specific patterns in each of the 6 isoacceptor families (tRNAMet, tRNAPhe, tRNALeu, tRNASer, tRNAVal and tRNAGly) where enough sequences are known to apply the test. The number of positions showing such a pattern ranged from 6 in the tRNASer and tRNAVal families to 15 in the tRNAMet, which is mostly formed of initiator tRNAs. Seven positions (12, 22, 31, 39, 44, 59 and 73) showed homologies in at least four families. The localization of most homologous nucleotides on the tRNA molecule makes it plausible that they interact with the recognition of the aminoacyl tRNA synthetase or, in a few cases, with the anticodon-codon recognition. A few positions (44, 59, 63) show homologies which are difficult to explain by a common functional constraint according to current ideas on the structure and function of tRNAs.