The tmRNA Website: invasion by an intron

Abstract

tmRNA (also known as 10Sa RNA or SsrA) plays a central role in an unusual mode of translation, whereby a stalled ribosome switches from a problematic mRNA to a short reading frame within tmRNA during translation of a single polypeptide chain. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA Website, a collection of sequences for tmRNA and the encoded proteolysis-inducing peptide tags, alignments, careful documentation and other information; the URL is http://www.indiana.edu/~tmrna. Four pseudoknots are usually present in each tmRNA, so the database is rich with information on pseudoknot variability. Since last year it has doubled (227 tmRNA sequences as of September 2001), a sequence alignment for the tmRNA cofactor SmpB has been included, and genomic data for Clostridium botulinum has revealed a group I (subgroup IA3) intron interrupting the tmRNA T-loop.

Figure 1

Intron in the C.botulinum tmRNA. (A) Standard secondary structure of the presumed post-splicing tmRNA; tag reading frame in lower case. The alanine charging tmRNA and the protein product of tmRNA translation are indicated. (B) Canonical features of group IA3 intron. Lower case, exon sequence; outline, bases highly conserved among group I introns; triangles, splice sites; dotted lines: proposed tetraloop–receptor interactions; rounded boxes, P10 partners. Sequence data from the Sanger Centre (http://www.sanger.ac.uk).

Figure 2

Effect of group I introns interrupting tRNA and tmRNA loops on the flanking stems. A generic 7 nt loop shows intron positions in tRNAs (subgroup IC3 in anticodon loops) or tmRNA (subgroup IA3 in T-loop). RNAs are shown at a stage between the two splicing steps, with intron in upper case and thick lines, and exons in lower case and thin line. Satisfying proposed P10 (rounded box) and P1 (unboxed) pairings comes at the expense of tRNA stem pairing (boxed) in some cases. Scytonema hofmanni tRNA^fMet (28); Anabaena PCC7120 tRNA^Leu (29); Agrobacterium tumefaciens tRNA^Arg (29); Azoarcus sp. tRNA^Ile (29).