Evidence that two present-day components needed for the genetic code appeared after nucleated cells separated from eubacteria.

Abstract

The trinucleotide/amino acid relationships of the present-day genetic code are established by the aminoacylation reactions of tRNA synthetases, whereby each of 20 specific amino acids is attached to its cognate tRNAs, which bear anticodon trinucleotides. Because of its universality, the appearance of the modern genetic code is thought to predate the separation of prokaryotic and eukaryotic organisms in the universal phylogenetic tree. In the light of new sequence information, we present here a phylogenetic analysis that shows an unusual picture for tyrosyl-and tryptophanyl-tRNA synthetases. In particular, the eukaryotic tyrosyl-and tryptophanyl-tRNA synthetases are more related to each other than to their respective prokaryotic counterparts. In contrast, each of the other 18 eukaryotic synthetases is more related to its prokaryotic counterpart than to any eukaryotic synthetase specific for a different amino acid. Our results raise the possibility that present day tyrosyl-and tryptophanyl-tRNA synthetases appeared after the separation of nucleated cells from eubacteria. The results have implications for the development of the genetic code.An open question concerning the origin of life is the mechanism of development of the genetic code and the role played by aminoacyl-tRNA synthetases (1). Because of their central role in linking amino acids with nucleotide triplets contained in transfer RNAs (2-6), aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. In agreement with this view of an ancient origin for the enzymes, all phylogenetic analyses carried out so far have determined that the sequences of tRNA synthetases cluster together by their amino acid specificities, and not by their positions in the phylogenetic tree (7-9). This observation clearly indicates that the enzymes appeared and evolved into their current types before the branching of the three Urkingdoms (eubacteria, archaebacteria, and eukaryotes). These previous analyses, however, were limited by the lack of (mainly) eukaryotic sequences for some of the enzymes. For instance, no eukaryotic tyrosyl-tRNA synthetase (YRS) or tryptophanyl-tRNA synthetase (WRS) had been analyzed. Here we present an analysis of the phylogenetic relationships between the prokaryote and eukaryote forms of this pair of enzymes.Recent determination by Carter and coworkers (10) of the crystal structure of a eubacterial WRS (B-WRS) revealed a high degree of structural similarity between this enzyme and the eubacterial YRS (B-YRS) solved by Brick et al. (11), thus suggesting a surprisingly recent common ancestor not discernible through sequence analysis. This structural conservation is particularly remarkable considering the vast amount of time since both of these class I tRNA synthetases separated from their ancestor. No three-dimensional information is available for any eukaryotic WRS or YRS (E-WRS or E-YRS).The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby...

Human Tyrosyl-tRNA Synthetase Shares Amino Acid Sequence Homology with a Putative Cytokine

“…These results are in good agreement with previously published comparisons between bacterial and eukaryotic tyrosyl-tRNA synthetases (17)(18)(19)(20)(21). Similar species specificity has also been observed for several other aminoacyl-tRNA synthetases (55)(56)(57)(58)(59) and is consistent with the hypothesis that the recognition of tRNA by aminoacyl-tRNA synthetases was still evolving after the divergence of bacteria and eukaryotes (39). The observation that tyrosyl-tRNA synthetase from the archaeon M. jannaschii lacks a substantial portion of the tRNA anticodon recognition domain suggests that the archaea may recognize and bind tRNA Tyr in a manner distinct from that found in both bacteria and eukaryotes.…”

“…Clones 186313, 151265, and 160622 contain full-length cDNA sequences, clone 109082 is missing the first 181 nucleotides of the coding sequence, clone 132369 is missing the first 792 nucleotides of the coding sequence, clone 53277 is missing the first 426 nucleotides of the coding sequence, and the nucleotide sequence of clone 124918 corresponds to that of the human tyrosyl-tRNA synthetase cDNA coding sequence through nu-cleotide 685, and then diverges into an unrelated sequence. In all of the cDNA clones examined (with the exception of the truncated clone 124918), the nucleotide sequence differs from the previously reported cDNA sequence for human tyrosyltRNA synthetase 5 (39) by the insertion of a cytosine at position 1061. This additional nucleotide base alters the reading frame of the cDNA sequence, which extends the open reading frame an additional 525 nucleotides.…”

Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains

“…6, which is published as supporting information on the PNAS web site). The generated phylogenetic tree is closer to the early one of Brown et al (26) than to that of Ribas de Pouplana et al (27), both of which lacked the structural information on eukaryotic TyrRS and TrpRS, and the many sequences now available. The bootstrap frequencies are exceptionally robust and consistent through the different phylogenetic methods used, thereby giving high confidence to the tree that was generated.…”

Comparison of the Catalytic Roles Played by the KMSKS Motif in the Human and Bacillus stearothermophilus Tyrosyl-tRNA Synthetases

“…Why Is the Second Lysine Absent from the KMSSS Sequence?-In eukaryotic tyrosyl-and tryptophanyl-tRNA synthetases, the second lysine in the KMSKS motif is replaced by either a serine or an alanine residue (28,29). Given the role that Lys-233 plays in the catalysis of tyrosine activation in the B. stearothermophilus enzyme it is interesting that it is not conserved in the human tyrosyl-tRNA synthetase.…”