Structural organization of Escherichia coli tmRNA.

A secondary structure of Escherichia coli 10Sa RNA (tmRNA) recently proposed on the basis of a variety of chemical and enzymatic probing data combined with phylogenetic analysis (Felden et al, in press), indicates a highly folded structure. Several long-range interactions including pseudoknots are proposed based on comparative analysis of 10 tmRNA genes. Whereas most of the probing data support these predicted secondary structures, several atypical reactivities in specific domains of the molecule suggest structural dynamics, perhaps relating to the complex functions of the molecule as both tRNA and mRNA. The structure of tmRNA has three modular units; a tRNA-like domain, an mRNA-like domain and an intricate connecting unit probably responsible for correct orientation of the two functional parts of the molecule.