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Background   Trans- translation releases stalled ribosomes from truncated mRNAs and tags defective proteins for proteolytic degradation using transfer-messenger RNA (tmRNA). This small stable RNA represents a hybrid of tRNA- and mRNA-like domains connected by a variable number of pseudoknots. Comparative sequence analysis of tmRNAs found in bacteria, plastids, and mitochondria provides considerable insights into their secondary structures. Progress toward understanding the molecular mechanism of template switching, which constitutes an essential step in  trans- translation, is hampered by our limited knowledge about the three-dimensional folding of tmRNA.    Results  To facilitate experimental testing of the molecular intricacies of  trans- translation, which often require appropriately modified tmRNA derivatives, we developed a procedure for building three-dimensional models of tmRNA. Using comparative sequence analysis, phylogenetically-supported 2-D structures were obtained to serve as input for the program ERNA-3D. Motifs containing loops and turns were extracted from the known structures of other RNAs and used to improve the tmRNA models. Biologically feasible 3-D models for the entire tmRNA molecule could be obtained. The models were characterized by a functionally significant close proximity between the tRNA-like domain and the resume codon. Potential conformational changes which might lead to a more open structure of tmRNA upon binding to the ribosome are discussed. The method, described in detail for the tmRNAs of  Escherichia coli ,  Bacillus anthracis , and  Caulobacter crescentus , is applicable to every tmRNA.    Conclusion  Improved molecular models of biological significance were obtained. These models will guide in the design of experiments and provide a better understanding of  trans- translation. The comparative procedure described here for tmRNA is easily adopted for the modeling the members of other RNA families.

Comparative 3-D Modeling of tmRNA