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tmRDB

http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html

Zwieb, C1, Gorodkin, J2, Knudsen, B3, Burks, J1, Wower, J4

1Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, U.S.A.
2Division of Genetics, The Royal Veterinary and Agricultural University, Institute of Animal Science and Animal Health, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark
3Bioinformatics Research Center, University of Aarhus, H¿egh Guldbergsgade 10, DK-8000 Aarhus C, Denmark
4Department of Animal and Dairy Sciences, Program in Cellular and Molecular Biosciences, Auburn University, Auburn, AL 36849-5415, U.S.A.

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. To serve as a tool in the study of structure and function of tmRNA, the tmRNA database (tmRDB) provides the known tmRNA sequences ordered alphabetically and phyogenetically with links to the primary sources, as well as a manually-checked alignment in various formats. The alignment provides the basis for phylogenetcally-supported tmRNA secondary structures and allows to identify covariations thus proving significant tertiary interactions. Three-dimensional models in pdb format generated by ERNA-3D [2] provide opportunities for testing interactions between tmRNA and protein cofactors (e.g. protein SmpB, ribosomal protein S1, EF-Tu) and ribosomes . Aligned sequences of tmRNA-encoded tag-peptides which serve as signals for cellular proteases are included in the database. Relevant information about proteins (SmpB, ribosomal protein S1, Alanyl-tRNA Synthetase and Elongation Factor Tu) known to interact with tmRNA, has been added. The tmRDB is curated 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/). tmRDB is updated regularly at least once a year.

Recent Developments

186 new tmRNAs from 10 bacterial groups for a total of 274 tmRNA sequences have been added.

Acknowledgements

We thank Florian MŸller for ERNA-3D and Ingolf Sommer for VCMD software. 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

Category   RNA Sequences

Go to the abstract in the NAR 2003 Database Issue.

 

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