Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications
- 1 December 2009
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 16 (1), 141-153
- https://doi.org/10.1261/rna.1745910
Abstract
It has been suggested that tRNA acceptor stems specify an operational RNA code for amino acids. In the last 20 years several attributes of the putative code have been elucidated for a small number of model organisms. To gain insight about the ensemble attributes of the code, we analyzed 4925 tRNA sequences from 102 bacterial and 21 archaeal species. Here, we used a classification and regression tree (CART) methodology, and we found that the degrees of degeneracy or specificity of the RNA codes in both Archaea and Bacteria differ from those of the genetic code. We found instances of taxon-specific alternative codes, i.e., identical acceptor stem determinants encrypting different amino acids in different species, as well as instances of ambiguity, i.e., identical acceptor stem determinants encrypting two or more amino acids in the same species. When partitioning the data by class of synthetase, the degree of code ambiguity was significantly reduced. In cryptographic terms, a plausible interpretation of this result is that the class distinction in synthetases is an essential part of the decryption rules for resolving the subset of RNA code ambiguities enciphered by identical acceptor stem determinants of tRNAs acylated by enzymes belonging to the two classes. In evolutionary terms, our findings lend support to the notion that in the pre-DNA world, interactions between tRNA acceptor stems and synthetases formed the basis for the distinction between the two classes; hence, ambiguities in the ancient RNA code were pivotal for the fixation of these enzymes in the genomes of ancestral prokaryotes.Keywords
This publication has 70 references indexed in Scilit:
- Enzyme Structure with Two Catalytic Sites for Double-Sieve Selection of SubstrateScience, 1998
- A Euryarchaeal Lysyl-tRNA Synthetase: Resemblance to Class I SynthetasesScience, 1997
- On the Origin of the Genetic CodeJournal of Theoretical Biology, 1997
- Species-specific tRNA recognition in relation to tRNA synthetase contact residuesJournal of Molecular Biology, 1997
- Was it an ancient gene codifying for a hairpin RNA that, by means of direct duplication, gave rise to the primitive tRNA molecule?Journal of Theoretical Biology, 1995
- Transfer RNA: From minihelix to genetic codeCell, 1995
- Molecular Recognition of the Identity-determinant Set of Isoleucine Transfer RNA from Escherichia coliJournal of Molecular Biology, 1994
- Rules that Govern tRNA Identity in Protein SynthesisJournal of Molecular Biology, 1993
- Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifsNature, 1990
- A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coliPure and Applied Chemistry, 1989