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Nucleic Acids Research, 2002, Vol. 30, No. 9 2025-2030
© 2002 Oxford University Press

Descent of a split RNA

Kelly P. Williams*

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

tmRNA is found in the usual one-piece form in most cyanobacteria, but a small clade has an unusual two-piece form, resulting from processing of a circularly permuted precursor RNA. Here, the secondary structure of the cyanobacterial one-piece tmRNA is established by phylogenetic sequence comparison; it deviates from most tmRNAs in having an extra (fifth) pseudoknot and a branched structure at the end of the tag reading frame. Patterns of sequence conservation between the two cyanobacterial tmRNA types suggest particular events in the evolution of the two-piece form. A simple gene permutation model of tandem duplication followed by loss of the outermost segments appears inadequate. An additional rearrangement is proposed, in which a structure impaired by deletion was regenerated at the expense of a neighboring structure.

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


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