© 2000 Oxford University Press
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tmRDB (tmRNA database) Christian Zwieb* and Jacek Wower1 Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA and 1Department of Animal and Dairy Sciences, Program in Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849-5415, USA Received September 20, 1999; Accepted September 22, 1999
ABSTRACT The tmRNA database (tmRDB) is maintained at the University of Texas Health Science Center at Tyler, Texas, and is accessible on the WWW at URL http:// psyche.uthct.edu/dbs/tmRDB/tmRDB.html . A tmRDB mirror site is located on the campus of Auburn University, Auburn, Alabama, reachable at the URL http://www.ag.auburn.edu/mirror/tmRDB/ . Since April 1997, the tmRDB has provided sequences of tmRNA (previously called 10Sa RNA), a molecule present in most bacteria and some organelles. This release adds 17 new sequences for a total of 60 tmRNAs. Sequences and corresponding tmRNA-encoded tag peptides are tabulated in alphabetical and phylogenetic order. The updated tmRNA alignment improves the secondary structures of known tmRNAs on the level of individual basepairs. tmRDB also provides an introduction to tmRNA function in trans-translation (with links to relevant literature), a limited number of tmRNA secondary structure diagrams, and numerous three-dimensional models generated interactively with the program ERNA-3D. tmRDB TABLE OF CONTENTS • tmRNA sequences listed in alphabetical or phylogenetic order. • tmRNA alignment in html, text (90 columns), text (wide), postscript, pdf, EMBL, GenBank, msf or nbrf format • tmRNA secondary structures • tmRNA 3-D structure models • Predicted tmRNA encoded tag peptides listed in alphabetical or phylogenetic order • Tag peptide alignment in html, text, gif, pdf, postscript, EMBL, GenBank, msf or nbrf format • About tmRDB • What’s new • Overview • Links • Disclaimer tmRNA FUNCTION According to the trans-translation model of Escherichia coli (1), a ribosome remains associated with the 3-end of broken
mRNA, thus leaving the tRNA for the last functional codon in the ribosomal P-site and the nascent polypeptide chain incomplete. Alanine-charged tmRNA comes to the rescue by entering the ribosomal A-site and allows the ribosome to proceed onto the tag-peptide coding region of tmRNA. When the tmRNA-encoded stop is encountered, the ribosome releases tagged polypeptide to be degraded by cytoplasmic and periplasmic proteases (for reviews, see 2,3). tmRDB DESCRIPTION The tmRDB collects, analyzes and distributes tmRNA-related information (4). At the core of the database are tmRNA sequences compiled from a wide variety of bacterial species, including some organelles. For this update, tmRNA sequences were obtained by searching the scientific literature, annotations within GenBank records (5), and other secondary databases, such as the tmRNA website (6). A representative subset of 12 tmRNA sequences served as input for searching the primary databases using BLASTN (7). The 17 new tmRNAs (for a total of 60 sequences) were from the following species (ordered alphabetically): Bordetella pertussis, Chlamydia pneumoniae, Chlorobium tepidum, Clostridium difficile, Francisella tularensis, Guillardia theta chloroplast, Klebsiella pneumoniae, Mycobacterium avium, Mycobacterium bovis, Pasteurella multocida, Salmonella paratyphi, Salmonella typhimurium, Shewanella putrefaciens, Staphylococcus aureus, Streptococcus gordonii, Streptococcus mutans and Thalassiosira weissflogii chloroplast. Updated were the tmRNA sequences of Helicobacter pylori, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Thermus thermophilus. As expected, all sequences were of eubacterial origin, and no eukaryotic or archaeal sources received significant similarity scores. AlphaProteobacteria lack a recognizable tmRNA, as demonstrated by analysis of the completed genome of Rickettsia prowazekii and a systematic study of 58 additional tmRNA sequences (8). The new tmRNA sequences are aligned using described methods (9,10) to derive minimal secondary structures in which each base pair is supported by comparative sequence analysis (11). This approach is in contrast to energy calculation or other means to maximize the number of base pairs (6,12). Inclusion of the new sequences into the previous alignment (4) confirmed the existence of 16 helices (not all of which are realized in every tmRNA molecule), including the tRNA- and mRNA-like portions as well as the presence of four pseudoknots (pk1–pk4) (11). Local improvements in certain previously ambiguous regions were achieved. For example, in the region
*To whom correspondence should be addressed. Tel: +1 903 877 7689; Fax: +1 903 877 5731; Email:
[email protected]
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that precedes the ‘resume’ codon an invariant adenosine residue is located at position –4 (A86 in E.coli tmRNA). Also, weakly supported is a new helix (tentatively named helix 17) situated between pk2 and pk3 in the tmRNAs of Bordetella pertussi, Legionella pneumophilia and Desulfovibrio desulfuricans. The tmRDB shows the updated alignment in a variety of common formats (see Table of Contents, above). A printable PostScript file where RNA helices are numbered and highlighted is available. The tmRDB also provides an alignment of predicted tmRNA encoded tag peptides, numerous tmRNA secondary structure models, and tentative three-dimensional models in PDB format produced interactively with the RNA modeling software ERNA-3D (13). ACCESS The data are accessible freely for research purpose at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html and at the tmRDB mirror site (http://www.ag.auburn.edu/mirror/tmRDB/ ). Hardcopies of tmRNA and tag-peptide alignments are available by Email request to the first author at
[email protected] or through written contact. The last author can be contacted at the Email address
[email protected] . This article should be cited in research projects assisted by the use of tmRDB.
ACKNOWLEDGEMENT This work was supported by NIH grant GM-58267 to J.W. REFERENCES 1. Keiler,K.C., Waller,P.R.H. and Sauer,R.T. (1996) Science, 271, 990–993. 2. Muto,A., Ushida,C. and Himeno,H. (1998) Trends Biochem. Sci., 1, 25–29. 3. Gottesman,S., Roche,E., Zhou,Y. and Sauer,R.T. (1998) Genes Dev., 12, 1338–1347. 4. Wower,J. and Zwieb,C. (1999) Nucleic Acids Res., 27, 167. 5. Benson,D.A., Boguski,M.S., Lipman,D.J., Ostell,J. and Ouellette,B.F.F. (1998) Nucleic Acids Res., 26, 1–7. Updated article in this issue: Nucleic Acids Res. (2000), 28, 15–18. 6. Williams,K. (1999) Nucleic Acids Res., 27, 165–166. Updated article in this issue: Nucleic Acids Res. (2000), 28, 168. 7. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389–3402. 8. Felden,B., Gesteland,R.F. and Atkins,J.F. (1999) Biochim. Biophys. Acta, 1446, 145–148. 9. Woese,C.R. and Fox,G.E. (1977) Proc. Natl Acad. Sci. USA, 74, 5088–5090. 10. Larsen,N. and Zwieb,C. (1991) Nucleic Acids Res., 19, 209–215. 11. Zwieb,C., Wower,I. and Wower,J. (1999) Nucleic Acids Res., 27, 2063–2071. 12. Williams,K. and Bartel,D. (1996) RNA, 2, 1306–1310. 13. Müller,F., Döring,T., Erdemir,T., Greuer,B., Jünke,N., Osswald,M., Rinke-Appel,L., Stade,K., Thamm,S. and Brimacombe,R. (1995) Biochem. Cell Biol., 73, 767–773.
