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Nucleic Acids Research, 2002, Vol. 30, No. 4 866-875
© 2002 Oxford University Press

Survey and Summary

Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies

Kelly P. Williams*

Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA

Most classical integrases of prokaryotic genetic elements specify integration into tRNA or tmRNA genes. Sequences shared between element and host integration sites suggest that crossover can occur at any of three sublocations within a tRNA gene, two with flanking symmetry (anticodon-loop and T-loop tDNA) and the third at the asymmetric 3' end of the gene. Integrase phylogeny matches this classification: integrase subfamilies use exclusively either the symmetric sublocations or the asymmetric sublocation, although tRNA genes of several different aminoacylation identities may be used within any subfamily. These two familial sublocation preferences imply two modes by which new integration site usage evolves. The tmRNA gene has been adopted as an integration site in both modes, and its distinctive structure imposes some constraints on proposed evolutionary mechanisms.

* Tel: +1 812 856 5697; Fax: +1 812 855 6705; Email: kwilliam{at}bio.indiana.edu


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