tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features

a1 Service de Biochimie et de Génétique Moléculaire, Bât 144, CEA/Saclay, 91191 Gif-sur-Yvette, France
a2 Laboratoire d'Enzymologie et Biochimie Structurales, Bât 34, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France


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.

(Received May 30 2002)
(Revised June 28 2002)
(Accepted July 12 2002)

Key Words: comparative genomics; matching pattern; RNomics; tRNA.

c1 Reprint requests to: Christian Marck, Service de Biochimie et de Génétique Moléculaire, Bât. 144, CEA/Saclay, F-91191 Gif-sur-Yvette CEDEX, France; e-mail: christian.marck@cea.fr