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The tmRNA website

http://www.indiana.edu/~tmrna

Description :
tmRNA (also known as 10Sa RNA or SsrA) plays a central role in an unusual process termed trans-translation, whereby a stalled ribosome switches from a problematic mRNA to a short reading frame within tmRNA during translation of a single polypeptide. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA Website, a collection of sequences, secondary structures and other information. Four pseudoknots are usually present in each tmRNA, so the database is rich with information on pseudoknot variability. An interesting variation on tmRNA structure is the two-piece form that results from circular permutation of the gene, which has evolved independently in two separate bacterial lineages. Ongoing genome sequencing projects are diligently monitored, and the database is updated frequently throughout the year.

tmRDB

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

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 develoments :
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.

Aknowledgement :
We thank Florian Mčller 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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