Database Commons

a catalog of worldwide biological databases

Genes for the RNA tmRNA and protein SmpB, partners in the trans-translation process that rescues stalled ribosomes, have previously been found in all bacteria and some organelles. During a major update of The tmRNA Website (relocated to http://bioinformatics.sandia.gov/tmrna), including addition of an SmpB sequence database, we found some bacteria that lack functionally significant regions of SmpB. Three groups with reduced genomes have lost the central loop of SmpB, which is thought to improve alanylation and EF-Tu activation: Carsonella, Hodgkinia, and the hemoplasmas (hemotropic Mycoplasma). Carsonella has also lost the SmpB C-terminal tail, thought to stimulate the decoding center of the ribosome. We validate recent identification of tmRNA homologs in oomycete mitochondria by finding partner genes from oomycete nuclei that target SmpB to the mitochondrion. We have moreover identified through exhaustive search a small number of complete, but often highly derived, bacterial genomes that appear to lack a functional copy of either the tmRNA or SmpB gene (but not both). One Carsonella isolate exhibits complete degradation of the tmRNA gene sequence yet its smpB shows no evidence for relaxed selective constraint, relative to other genes in the genome. After loss of the SmpB central loop in the hemoplasmas, one subclade apparently lost tmRNA. Carsonella also exhibits gene overlap such that tmRNA maturation should produce a non-stop smpB mRNA. At least some of the tmRNA/SmpB-deficient strains appear to further lack the ArfA and ArfB backup systems for ribosome rescue. The most frequent neighbors of smpB are the tmRNA gene, a ratA/rnfH unit, and the gene for RNaseR, a known physical and functional partner of tmRNA-SmpB.

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.

tmRNA (10Sa RNA) has a central role in trans -translation, in which a peptide tag encoded in tmRNA is added to the abnormally short protein product of a broken mRNA, as a signal for proteolysis of the entire tagged protein. The tmRNA website was established in 1997 as a resource for phylogenetic considerations of tmRNA structure and function. Since then, three partial tmRNA sequences have been completed, and sequences from 13 more species have been identified. Forty-six species from 10 bacterial phyla and chloroplasts are now represented in the database. Provisional sequence alignments and predicted proteolysis tag sequences are provided, as well as a literature review and a guide to searching for new tmRNA sequences. The tmRNA website is accessible via WWW at a new URL: http://sunflower.bio.indiana.edu/kwilliam/tmRNA /home.html