title: tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter.
abstract: A general mechanism in bacteria to rescue stalled ribosomes and to clear the cell of incomplete polypeptides involves an RNA species, tmRNA (SsrA), which functions as both a tRNA and an mRNA. This RNA encodes a peptide tag that is incorporated at the end of the aberrant polypeptide and targets it for proteolysis. We have identified a circularly permuted version of the tmRNA gene in alpha-proteobacteria as well as in a lineage of cyanobacteria. The genes in these two groups seem to have arisen from two independent permutation events. As a result of the altered genetic structure, these tmRNAs are composed of two distinct RNA molecules. The mature two-piece tmRNAs are predicted to have a tRNA-like domain and an mRNA-like domain similar to those 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 genome 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 crescentus produces a functional two-piece tmRNA.
authors.affiliation: Department of Developmental Biology, Stanford University, B343 Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA.
authors.forename: K C
authors.initials: KC
authors.lastname: Keiler
authors.forename: L
authors.initials: L
authors.lastname: Shapiro
authors.forename: K P
authors.initials: KP
authors.lastname: Williams
mesh_terms: D020561:Alphaproteobacteria / Q000235:genetics; D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D016935:Caulobacter crescentus / Q000235:genetics* / Q000378:metabolism; D000458:Cyanobacteria / Q000235:genetics; D008928:Mitochondria / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011499:Protein Processing, Post-Translational; D012323:RNA Processing, Post-Transcriptional; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger; C096222:tmRNA; D012343:RNA, Transfer