From 50 genomes of the three domains of life (7 eukarya, 13
archaea, and 30 bacteria), we extracted, analyzed, and compared
over 4,000 sequences corresponding to cytoplasmic, nonorganellar
tRNAs. For each genome, the complete set of tRNAs required to
read the 61 sense codons was identified, which permitted revelation
of three major anticodon-sparing strategies. Other features
and sequence peculiarities analyzed are the following: (1) fit
to the standard cloverleaf structure, (2) characteristic consensus
sequences for elongator and initiator tDNAs, (3) frequencies
of bases at each sequence position, (4) type and frequencies
of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages
and anticodon-sparing strategies, (6) identification of the
tRNA-Ile with anticodon CAU reading AUA, (7) size of variable
arm, (8) occurrence and location of introns, (9) occurrence
of 3′-CCA and 5′-extra G encoded at the tDNA level,
and (10) distribution of the tRNA genes in genomes and their
mode of transcription. Among all tRNA isoacceptors, we found
that initiator tDNA-iMet is the most conserved across the three
domains, yet domain-specific signatures exist. Also, according
to which tRNA feature is considered (5′-extra G encoded
in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU,
presence of intron, absence of “two-out-of-three”
reading mode and short V-arm in tDNA-Tyr) Archaea sequester
either with Bacteria or Eukarya. No common features between
Eukarya and Bacteria not shared with Archaea could be unveiled.
Thus, from the tRNomic point of view, Archaea appears as an
“intermediate domain” between Eukarya and Bacteria.