tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter

A general mechanism in bacteria to rescue stalled ribosomes and to clear th e cell of incomplete polypeptides involves an RNA species, tmRNA (SsrA), wh ich functions as both a tRNA and an mRNA. This RNA encodes a peptide tag th at is incorporated at the end of the aberrant polypeptide and targets it fo r proteolysis. We have identified a circularly permuted version of the tmRN A gene in alpha-proteobacteria as well as in a lineage of cyanobacteria, Th e genes in these two groups seem to have arisen from two independent permut ation events. As a result of the altered genetic structure, these tmRNAs ar e composed of two distinct RNA molecules. The mature two-piece tmRNAs are p redicted to have a tRNA-like domain and an mRNA-like domain similar to thos e of standard one-piece tmRNAs, with a break located in the loop containing the tag reading frame. A related sequence was found in the mitochondrial g enome of Reclinomonas americana, but only the tRNA-like portion is retained . Although several sequence and structural motifs that are conserved among one-piece tmRNAs have been lost, the alpha-proteobacterium Caulobacter cres centus produces a functional two-piece tmRNA.