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tmRDB


NAR Molecular Biology Database Collection entry number 250
Burks, J1, Zwieb, C2, Gorodkin, J3, Knudsen, B4 and Wower, J4
1Department of Animal and Dairy Sciences, Program in Cellular and Molecular Biosciences, Auburn University, Auburn, AL 36849-5415, U.S.A.
2Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, U.S.A.
3Division of Genetics, The Royal Veterinary and Agricultural University, Institute of Animal Science and Animal Health, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark
4Bioinformatics Research Center, University of Aarhus, H¿egh Guldbergsgade 10, DK-8000 Aarhus C, Denmark
Contact zwieb@uthct.edu

Database Description

tmRNA is a molecule that combines functions of tRNA and mRNA in a process called trans-translation [see 1, for review] to rescue ribosomes that are stalled at the end of broken mRNA. tmRNA-like sequences have been identified in all bacteria analyzed to date including mitochondria, chloroplasts, and cyanelles. Recently, tmRNA-like molecules have been discovered also in certain bacteriphages. To assist in the study of structure and function of tmRNA, the tmRNA database (tmRDB) lists the known tmRNA sequences ordered alphabetically and phylogenetically with links to the primary sources. The tmRNA alignment, available in various formats, is the basis for supported tmRNA secondary structures. Three-dimensional models in pdb format generated by ERNA-3D [2] help to investigate potential interactions between the tmRNA and its cofactors. Aligned sequences of tmRNA-encoded tag-peptides which serve as signals for cellular proteases, are included. The tmRDB also provides relevant information about the proteins known to interact with tmRNA such as SmpB, ribosomal protein S1, alanyl-tRNA synthetase, and elongation factor Tu,. The tmRDB is maintained at the University of Texas Health Science Center at Tyler, Texas, and accessible on the World Wide Web at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html. Mirror sites are located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Institute of Biological Sciences, Aarhus, Denmark (http://www.bioinf.au.dk/tmRDB/).

Recent Developments

As of October 2004, of the 123 new tmRNA sequences (a total of 396 tmRNAs), three are of bacteriophage, 13 of chloroplast, and five of mitochondrial origin.

Acknowledgements

We thank Florian MŸller for ERNA-3D. J.G. is supported by the Danish Technical Research Council and the Ministry of Food, Agriculture and Fisheries. This work was supported by NIH grant GM-58267 to J.W.

References

[1] Karzai, A.W., E.D. Roche and R.T. Sauer (2000) The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat. Struct. Biol. 7:449-455
[2] MÜller, F., DÖring, T., Erdemir, T., Greuer, B., JÜnke, N., Osswald, M., Rinke-Appel, L., Stade, K., Thamm, S., and Brimacombe, R. (1995) Getting closer to an understanding of the three-dimensional structure of ribosomal RNA. Biochem. Cell Biol., 73, 767-773


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