The tmRDB and SRPDB resources

Abstract

Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Royal Veterinary and Agricultural University, Denmark (http://tmrdb.kvl.dk/). The signal recognition particle database (SRPDB) at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html is mirrored at http://srpdb.kvl.dk/ and the University of Goteborg (http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html). The databases assist in investigations of the tmRNP (a ribonucleoprotein complex which liberates stalled bacterial ribosomes) and the SRP (a particle which recognizes signal sequences and directs secretory proteins to cell membranes). The curated tmRNA and SRP RNA alignments consider base pairs supported by comparative sequence analysis. Also shown are alignments of the tmRNA-associated proteins SmpB, ribosomal protein S1, alanyl-tRNA synthetase and Elongation Factor Tu, as well as the SRP proteins SRP9, SRP14, SRP19, SRP21, SRP54 (Ffh), SRP68, SRP72, cpSRP43, Flhf, SRP receptor (alpha) and SRP receptor (beta). All alignments can be easily examined using a new exploratory browser. The databases provide links to high-resolution structures and serve as depositories for structures obtained by molecular modeling.

Figure 1

Schematic representation of the secondary structures of (A) E.coli tmRNA and (B) SRP RNA. The tRNA-like (TLD), mRNA-like (MLD) and pseudoknot (PKD) domains are indicated. Helices and their sections are numbered from 1 to 12 and letters a–d. The four pseudoknots are labeled pk1–pk4. The tag peptide-encoding region is located between the resume and stop codon as indicated. Conserved regions are indicated by dashed lines. In the SRP RNA secondary structure diagram B, the features of the mammalian SRP RNA are shown in gray. Helices are numbered from 1 to 12 with helical sections labeled with letters a–f. The approximate boundaries of the small (Alu) and the large (S) domain are shown. The recently discovered extra helix (E) in the SRP RNAs of some Pezizomycotina (see Table 2) is indicated by the arrowhead. Conserved regions are indicated by dashed lines. The conservations are highlighted in the html- and png-formatted alignment files available at the tmRDB and SRPDB, respectively.