Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves

Randau, Lennart
Münch, Richard
Hohn, Michael J.
Jahn, Dieter
Söll, Dieter

¹Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
²Institut für Mikrobiologie, Technical University Braunschweig, P.O. Box 3329, D-38023 Braunschweig, Germany
³Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
⁴Department of Chemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520-8114, USA

Received 30 August; accepted 2 December 2004; doi:10.1038/nature03233.

Correspondence and requests for materials should be addressed to D.S.

Nature 433(7025):p 537-541, February 3, 2005.

Analysis of the genome sequence of the small hyperthermophilic archaeal parasiteNanoarchaeum equitanshas not revealed genes encoding the glutamate, histidine, tryptophan and initiator methionine transfer RNA species. Here we develop a computational approach to genome analysis that searches for widely separated genes encoding tRNA halves that, on the basis of structural prediction, could form intact tRNA molecules. A search of theN. equitansgenome reveals nine genes that encode tRNA halves; together they account for the missing tRNA genes. The tRNA sequences are split after the anticodon-adjacent position 37, the normal location of tRNA introns. The terminal sequences can be accommodated in an intervening sequence that includes a 12-14-nucleotide GC-rich RNA duplex between the end of the 5′ tRNA half and the beginning of the 3′ tRNA half. Reverse transcriptase polymerase chain reaction and aminoacylation experiments ofN. equitanstRNA demonstrated maturation to full-size tRNA and acceptor activity of the tRNA^Hisand tRNA^Gluspecies predictedin silico.As the joining mechanism possibly involves tRNAtrans-splicing, the presence of an intron might have been required for early tRNA synthesis.