Two types of aminoacyl-trna synthetases could be originally encoded by complementary strands of the same nucleic ACID

Abstract

The lack of even a marginal similarity between the two aminoacyl-tRNA synthetase (aaRS) classes suggests their independent origins (Eriani et al., 1990; Nagel and Doolittle, 1991). Yet, this independence is a puzzle inconsistent with the common origin of transfer RNAs, the coevolutionary theory of the genetic code (Wong, 1975, 1981) and other associated data and ideas. We present here the results of antiparallel 'class I versus class II' comparisons of aaRSs within their signature sequences. The two main HIGH- and KMSKS-containing motifs of class I appeared to be complementary to the class II motifs 2 and 1, respectively. The above sequence complementarity along with the mirror-image between crystal structures of complexes formed by the opposite aaRSs and their cognate tRNAs (Ruff et al., 1991), and the generally mirror ('head-to-tail') mapping of the basic functional sites in the sequences of aaRSs from the opposite two classes led us to conclude that these two synthetases emerged synchronously as complementary strands of the same primordial nucleic acid. This conclusion, combined with the hypothesis of tRNA concerted origin (Rodin et al., 1993a,b), may explain many intriguing features of aaRSs and favor the elucidation of the origin of the genetic code.

Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene

“…1 (1, 2), established a strong posterior probability of the sense/antisense ancestry hypothesis (3,4) by verifying biochemical predictions of the hypothesis. Parallel structural evolution of the two families is consistent with a similar hierarchy over a 10 5 -fold range in catalytic proficiency.…”

“…Parallel structural evolution of the two families is consistent with a similar hierarchy over a 10 5 -fold range in catalytic proficiency. We deconstructed members of both aaRS 4 superfamilies to reveal structurally invariant cores that are relatively free of insertions and deletions that would rule out such coding (5,6). These "Urzymes" (from Ur ϭ primitive) contain the most highly conserved 120 -130-amino acid fragments from the two superfamilies.…”

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.…”

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

“…Another link is the fact that structural homologs of both Class I and Class II aaRSs have been found as proteins associated with the replication (e.g., bacterial dnaG primase and the beta subunit of mitochondrial polymerase, respectively, see Carrodeguas et al 1999). Also, it has been suggested (Rodin and Ohno 1995;Carter and Duax 2002) that the two ancestors of Class I and Class II aaRSs were in fact originally encoded by the same gene on the two complementary strands. If true, the mechanism for ''switching class'' may be understood by a simple recombination event, assuming the gene was inserted between two inverted repeats.…”