Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases

Abstract

Class I and II aaRS recognition of opposite grooves was likely among the earliest determinants fixed in the tRNA acceptor stem bases. A new regression model identifies those determinants in bacterial tRNAs. Integral coefficients relate digital dependent to independent variables with perfect agreement between observed and calculated grooves for all twenty isoaccepting tRNAs. Recognition is mediated by the Discriminator base 73, the first base pair, and base 2 of the acceptor stem. Subsets of these coefficients also identically compute grooves recognized by smaller numbers of aaRS. Thus, the model is hierarchical, suggesting that new rules were added to pre-existing ones as new amino acids joined the coding alphabet. A thermodynamic rationale for the simplest model implies that Class-dependent aaRS secondary structures exploited differential tendencies of the acceptor stem to form the hairpin observed in Class I aaRS•tRNA complexes, enabling the earliest groove discrimination. Curiously, groove recognition also depends explicitly on the identity of base 2 in a manner consistent with the middle bases of the codon table, confirming a hidden ancestry of codon-anticodon pairing in the acceptor stem. That, and the lack of correlation with anticodon bases support prior productive coding interaction of tRNA minihelices with proto-mRNA.

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

“…Urzyme structures inferred from extant crystal structures suggest that ancestral secondary structural differences between the two synthetase classes do actually reinforce the acceptor‐stem structures observed in productive cocrystals . The Class I Urzyme Rossmann‐fold architecture creates a positively charged pocket for the A76 5′ phosphate at the N‐terminus of the “specificity‐determining helix” (Fig.…”

“…Codon-anticodon pairing in the acceptor stem may have allowed coded translation to begin before tRNAs acquired anticodons, along lines advocated by DiGiulio (18)(19)(20). Use of that pairing may also reflect a transitional mechanism for bidirectional coding via formation of triple helices (4).…”

“…to recognize the G3‐U70 base pair from both grooves . We have argued that this modification of the synthetase–tRNA complex involves more recently acquired domains, and hence that it evolved after the establishment and early expansion of the genetic code.…”

“…Groove recognition is dictated, surprisingly, by just the four topmost bases of the ancestral tRNA acceptor stem, which facilitate a hierarchical set of “rules” (Table ). We have reviewed here the evidence that the original cognate pairs resulted from a combination of thermodynamic conformational preferences induced by patterns of acceptor stem purines and pyrimidines in the topmost four bases that enable hairpin formation by tRNA acceptor stems of ancestral Class I aaRS, and class‐specific synthetase secondary structures in both classes that reinforced the resulting differential thermodynamic tendencies.…”

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

“…To address this question we used statistical regression methods, similar to those used to map the amino acid phase transfer free energies to the acceptor stem and anticodon (10,42), to show that this primordial differentiation is coded in the three topmost tRNA acceptor stem bases (3). As new amino acids entered the code, they overwrote that ancestral tRNA duality, turning the acceptorstem bases into a Palimpsest, derived from the Greek verb "psen", "to scrape out".…”