In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership

Abstract

Aminoacyl tRNA synthetases (aaRS) are grouped into Class I and II based on primary and tertiary structure and enzyme properties suggesting two independent phylogenetic lineages. Analogously, tRNA molecules can also form two respective classes, based on the class membership of their corresponding aaRS. Although some aaRS–tRNA interactions are not extremely specific and require editing mechanisms to avoid misaminoacylation, most aaRS–tRNA interactions are rather stereospecific. Thus, class-specific aaRS features could be mirrored by class-specific tRNA features. However, previous investigations failed to detect conserved class-specific nucleotides. Here we introduce a discrete mathematical approach that evaluates not only class-specific ‘strictly present’, but also ‘strictly absent’ nucleotides. The disjoint subsets of these elements compose a unique partition, named extended consensus partition (ECP). By analyzing the ECP for both Class I and II tDNA sets from 50 (13 archaeal, 30 bacterial and 7 eukaryotic) species, we could demonstrate that class-specific tRNA sequence features do exist, although not in terms of strictly conserved nucleotides as it had previously been anticipated. This finding demonstrates that important information was hidden in tRNA sequences inaccessible for traditional statistical methods. The ECP analysis might contribute to the understanding of tRNA evolution and could enrich the sequence analysis tool repertoire.

Mapping Hidden Potential Identity Elements by Computing the Average Discriminating Power of Individual tRNA Positions

“…18 Principles of the analysis and the algorithm remained the same. However, in this case, not the two AARS-based tRNA classes were compared, but all pairs of the 20 tRNA identity sets.…”

The evolution of the genetic code: Impasses and challenges

“…Here we need to mention, that sometimes identity element can be the absence of certain nucleotides at certain places (negative identity determinants), and not the presence of it as demonstrated for the class I and class II tRNA identity elements (Jakó et al, 2007). Discriminator / identity elements are important as the genetic code is "known" by the aminoacyl tRNA synthetases, the enzymes that attach the amino acid to the cognate tRNA.…”

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

“…The operational RNA code was initially a hypothetical proposal, essentially without details ( 2 , 6 ). Several subsequent efforts have failed to provide those details ( 7–9 ). An important analysis by Shaul ( 8 ) subsequently provided a comprehensive description in the form of complex trees whose branches are regression models that lead to decisions on classification.…”