Abstract
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.