The genetic code likely arose when a bidirectional gene replicating as a quasi‐species began to produce ancestral aminoacyl‐tRNA synthetases (aaRS) capable of distinguishing between two distinct sets of amino acids. The synthetase class division therefore necessarily implies a mechanism by which the two ancestral synthetases could also discriminate between two different kinds of tRNA substrates. We used regression methods to uncover the possible patterns of base sequences capable of such discrimination and find that they appear to be related to thermodynamic differences in the relative stabilities of a hairpin necessary for recognition of tRNA substrates by Class I aaRS. The thermodynamic differences appear to be exploited by secondary structural differences between models for the ancestral aaRS called synthetase Urzymes and reinforced by packing of aromatic amino acid side chains against the nonpolar face of the ribose of A76 if and only if the tRNA CCA sequence forms a hairpin. The patterns of bases 1, 2, and 73 and stabilization of the hairpin by structural complementarity with Class I, but not Class II, aaRS Urzymes appear to be necessary and sufficient to have enabled the generation of the first two aaRS–tRNA cognate pairs, and the launch of a rudimentary binary genetic coding related recognizably to contemporary cognate pairs. As a consequence, it seems likely that nonrandom aminoacylation of tRNAs preceded the advent of the tRNA anticodon stem‐loop. Consistent with this suggestion, coding rules in the acceptor‐stem bases also reveal a palimpsest of the codon–anticodon interaction, as previously proposed. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1088–1098, 2019

Because tRNA is the core biological intellectual property that was necessary to evolve translation systems, tRNAomes, ribosomes, aminoacyl-tRNA synthetases, and the genetic code, the evolution of tRNA is the core story in evolution of life on earth. We have previously described the evolution of type-I tRNAs. Here, we use the same model to describe the evolution of type-II tRNAs, with expanded V loops. The models are strongly supported by inspection of typical tRNA diagrams, measuring lengths of V loop expansions, and analyzing the homology of V loop sequences to tRNA acceptor stems. Models for tRNA evolution provide a pathway for the inanimate-to-animate transition and for the evolution of translation systems, the genetic code, and cellular life.

Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. For the first time, we extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric effects.EvolutionThe evolutionary origin of aaRSs is hard to track. Phylogenetic analyses of aaRS sequences show that they do not follow the standard model of life 14 ; the development of aaRSs was nearly complete before the Last Universal Common Ancestor (LUCA) 15,16 . Their complex evolutionary history included horizontal gene transfer, fusion, duplication, and recombination events 14, 17-21 . Sequence analyses 22 and subsequent structure investigations 23,24 revealed that aaRSs can be divided into two distinct classes (Class I and Class II) that share no similarities at sequence or structure level. Each of the classes is responsible for 10 of the 20 proteinogenic amino acids and can be further grouped into subclasses 15 . Most eukaryotic genomes contain the complete set of 20 aaRSs. However, some species lack certain aaRS-encoding genes and compensate for this by post-modifications 7, 25-27 or alternative pathways [28][29][30] . A scenario where Class I and Class II originated simultaneously from opposite strands of the same gene 31, 32 is among the most popular explanations for the origin of aaRSs. This so-called Rodin-Ohno hypothesis (named after Sergei N. Rodin and Susumu Ohno 31 ) is supported by experimental deconstructions of both aaRS classes [33][34][35] . At the dawn of life the concurrent duality could have allowed to implement an initial binary choice, which is the minimal requirement to establish any code 9 .Biochemical Function In order to fulfill their biological function aaRSs are required to catalyze two distinct reaction steps. Prior to its covalent attachment to the 3' end of the tRNA molecule, the designated amino acid is activated with adenosine triphosphate (ATP) and an aminoacyl-adenylate intermediate is formed 36,37 . In general, the binding sites of aaRSs can be divided into two moieties: the part where ATP is bound as well as the part where specific interactions with the amino acid ligand are established ( Fig. 1). Is is assumed that the amino acid activation with ATP constituted the principal kinetic barrier for the creation of peptides in the prebiotic context 35 . Due to the fundamental importance of this first reaction step, highly conserved sequence 4 and structural motifs 38 exist, which are likely to be vital for the aminoacylation reaction. While the activation of amino acids with ...