Analysis of tRNA abstract shapes of precursor/derivative amino acids in Archaea

Wong's theory of the genetic code's origin states that because of historical constraints, codon assignment depends on the relation between precursor and derivative amino acids, a result of the coevolutionary process between amino acids' biosynthetic pathways and tRNAs. Based on arguments supporting the assumption that natural selection favors more stable and thus functionally constrained structures, we tested whether precursor and derivative tRNAs are equally evolved by measuring their structural parameters, thermostability and molecular plasticity. We also estimated the extent to which precursor and derivative tRNAs differ within Archaea. We used Archaea sequences of both precursor and derivative tRNAs in order to examine the plastic repertoires or sets of suboptimal structures at a defined free energy interval. We grouped secondary structures according to their helix nesting and adjacency using abstract shapes analysis. This clustering enabled us to infer a consensus sequence for all shapes that fit the clover leaf secondary structure [Giegerich, R., et al., Nucleic Acids Res 2004; 32 (16): 4843-51.]. This consensus sequence was then folded in order to retrieve a set of suboptimal structures. For each pair of precursor and derivative tRNAs, we compared these plastic repertoires based on the number of secondary structures, the thermostability of the minimum free energy structure and two structural parameters (base pair propensity (P) and mean length of helical stem structures (S)), which were measured for every representative secondary structure [Schultes, E.A., et al., J Mol Evol 1999; 49 (1): 76-83.]. We found that derivative tRNAs have fewer numbers of shapes, higher thermostability and more stable parameters than precursor tRNAs, a fact in full agreement with Wong's coevolution theory of the genetic code.