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

Abstract

Analysis of the genome sequence of the small hyperthermophilic archaeal parasite Nanoarchaeum equitans1,2 has 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 the N. equitans genome 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 of N. equitans tRNA demonstrated maturation to full-size tRNA and acceptor activity of the tRNAHis and tRNAGlu species predicted in silico. As the joining mechanism possibly involves tRNA trans-splicing, the presence of an intron might have been required for early tRNA synthesis.

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Figure 1: Predicted split N. equitans tRNA genes.
Figure 2: RT–PCR amplification of the newly identified tRNAs in N. equitans.
Figure 3: Aminoacylation of unfractioned N. equitans tRNA by N. equitans glutamyl-tRNA synthetase and histidyl-tRNA synthetase.
Figure 4: Schematic representation of a 5′ tRNA half gene (tRNAGlu) and the corresponding 3′ tRNA half gene found in N. equitans.

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Acknowledgements

We thank H. Huber and K. O. Stetter for advice and spirited discussions, M. Thomm for the use of laboratory facilities, and J. Yuan and J. Sabina for critically reading the manuscript. This work was supported by grants from the National Institute of General Medical Sciences and the Department of Energy (to D.S.) and by the German Federal Ministry of Education and Research (BMBF) for the Bioinformatics Competence Center ‘Intergenomics’ (to D.J.).

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Correspondence to Dieter Söll.

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Randau, L., Münch, R., Hohn, M. et al. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves. Nature 433, 537–541 (2005). https://doi.org/10.1038/nature03233

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