Abstract
The transfer-messenger RNA (tmRNA) and its partner protein SmpB act together in resolving problems arising when translating bacterial ribosomes reach the end of mRNA with no stop codon. Their genes have been found in nearly all bacterial genomes and in some organelles. The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has recently moved to http://bioinformatics.sandia.gov/tmrna/. New features include software used to find the sequences, an update raising the number of unique tmRNA sequences from 492 to 1716, and a database of SmpB sequences which are served along with the tmRNA sequence from the same organism.
Highlights
TmRNA is so-named for its dual tRNA-like and mRNA-like nature
A long disrupted stem (P2) exits the tRNA-like domain, capped by a large loop composed of a pseudoknot, the tag reading frame with the stop codon in the loop of a hairpin, and a string of three pseudoknots
The reading frame for all but the parenthetical alanyl residue of the tag was found in the E.coli tmRNA sequence
Summary
TmRNA ( known as 10Sa RNA) is so-named for its dual tRNA-like and mRNA-like nature. A half-tRNA structure, with a coaxially stacked T stem–loop and acceptor stem–tail, was identified in tmRNA upon determination of the ends of the Escherichia coli and Bacillus subtilis molecules and comparison with other available gene sequences [5,6]; the CCA tail is not always fully encoded in the genome, but has been found at the 3′ end of the B.subtilis tmRNA [6].
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