Structural Enzymology, Phylogenetics, Differentiation, and Symbolic Reflexivity at the Dawn of Biology

Translation of symbols in one chemical language into another defined genetics. Yet, the co-linearity of codons and amino acids is so commonplace an idea that few even ask how it arose. Readout is done by two distinct sets of proteins, called aminoacyl-tRNA synthetases. Aminoacyl-tRNA synthetases must enforce the rules first used to assemble themselves. To understand the roots of translation, we must experimentally test the structural codes that the earliest aminoacyl-tRNA synthetases used to recognize both amino acid and RNA substrates. We present here new results on five different facets of that problem. (i) The surfaces of structures coded by opposite strands of the same gene have opposite polarities. Core residues in proteins from one strand are surface residues in proteins from the other strand. The complementarity of base pairing thus projects into the proteome. That leads in turn to contrasting amino acid and RNA substrate binding modes. (ii) Escherichia coli reproduces in vivo a nested hierarchy of active excerpts, or "urzymes," similar to those we had designed as models for ancestral aminoacyl-tRNA synthetases. (iii) A third novel deletion produced in vivo and a new Class II urzyme suggest how to design bidirectional urzyme genes. (iv) Codon middle base pairing provides a basis to constrain Class I and II aminoacyl-tRNA synthetase family trees. (v) Aminoacyl-tRNA synthetase urzymes acylate class-specific subsets of an RNA library, showing urzyme RNA substrate specificity for the first time. Four new tree-building tools augment these results to compose a viable platform for experimental study of the origins of genetic coding.