Coding of Class I and II Aminoacyl-tRNA Synthetases

Abstract

SUMMARY The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels—protozymes and Urzymes—associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric—middle base-pairing frequencies in sense/antisense alignments—that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins.

Class I and II aminoacyl‐tRNA synthetase tRNA groove discrimination created the first synthetase–tRNA cognate pairs and was therefore essential to the origin of genetic coding

“…Experimental acylation of tRNA minihelices by full-length aaRSs led Schimmel, Giegé, Moras, and Yokoyama (44) to renew the earlier speculation (23) that aaRS catalytic domains and minihelices originally mediated protein synthesis according to a code residing entirely within the acceptor stem, which they called an "operational RNA code." AARS Urzymes (8,31,32,39,40) are substantially smaller than catalytic domains, and cannot recognize tRNA anticodons, but nevertheless acylate intact tRNAs (31), validating their proposal.…”

“…The phylogenetic (3,7,8,13,37) and biochemical (6,8,10,31,32,39,40) evidence is quite strong that codon-dependent translation and genetic coding began with the advent of ancestral synthetases with scarcely nonrandom specificities. Emergence of those ancestral aaRS also likely required the near simultaneous emergence of coded peptides that activated amino acids and aminoacylated tRNA.…”

Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code

“…As domains evolved to take on the appropriate fold, Zn-binding disappears from some domains that initially evolved around Zn binding (Figure 4). The more complex model that class I and class II aaRS enzymes arose from transcription and translation of an ancestral bi-directional gene [3–6] we find less likely. Early in evolution, Zn-binding appears to have directed the stability and folding conformations of large proteins such as aaRS enzymes and RNA polymerase.…”

“…As described previously, tRNA Pri evolved initially as an improved mechanism to synthesize polyglycine to stabilize protocells (as in bacterial cell walls) before the coevolution of tRNAomes, aaRS enzymes, ribosomes and the genetic code. Alternate views have been expressed by others [3,4,7,8,44]. …”

“…Class II aaRS, by strong contrast, have an active site of antiparallel β-sheets. The evolutionary relationship of class I and class II enzymes has not been clearly demonstrated, although the interesting suggestion has been made that class I and class II aaRS enzymes were encoded on opposing strands of a bi-directional ancestral gene [3–8]. We provide a simpler explanation.…”