A third lineage with two-piece tmRNA

Abstract

tmRNA combines tRNA and mRNA properties and helps bacteria to cope with stalled ribosomes. Its termini normally pair in the tRNA domain, closing the mRNA portion into a looping domain. A striking variation is a two-piece form that effectively breaks open the mRNA domain loop, resulting from independent gene permutation events in alphaproteobacteria and cyanobacteria. Convergent evolution to a similar form in separate bacterial lineages suggests that loop-opening benefits tmRNA function. This argument is strengthened by the discovery of a third bacterial lineage with a loop-opened two-piece tmRNA. Whereas most betaproteobacteria have one-piece tmRNA, a permuted tmRNA gene was found for Dechloromonas aromatica and close relatives. Correspondingly, two tmRNA pieces were identified, at approximately equal abundance and at a level one-fifteenth that of ribosomes, a 189 nt mRNA piece and a 65 nt aminoacylatable piece. Together these pieces were active with purified Escherichia coli translational components, but not alone. The proposed secondary structure combines common tmRNA features differently from the structures of other two-piece forms. The origin of the gene is unclear; horizontal transfer may be indicated by the similarity of the tRNA domain to that from a cyanobacterial two-piece tmRNA, but such transfer would not appear simple since the mRNA domain is most similar to that of other betaproteobacteria.

Escherichia coli tmRNA lacking pseudoknot 1 tags truncated proteins in vivo and in vitro

“…We demonstrated unambiguously that pk1 is not an essential component of tmRNA but plays an important role in stabilizing the structure of tmRNAs with long RNA segments connecting the TLD and MLD. Our findings are consistent with comparative analyses of tmRNA sequences, which revealed that in some tmRNAs pk1 could be replaced with either a single-stranded RNA or a single hairpin (Zwieb et al 1999;Gaudin et al 2002;Gueneau de Novoa and Williams 2004;Sharkady and Williams 2004;Andersen et al 2006).…”

“…These observations provided unambiguous proof that pk1 was not essential for trans-translation. Our finding is consistent with comparative analyses of tmRNA sequences that identified a number of bacterial tmRNAs, in which pk1 was replaced by a single hairpin Gaudin et al 2002;Sharkady and Williams 2004;Andersen et al 2006). In M. pneumoniae, P. marinus, and G. violaceus, the hairpin contained 5 bp.…”

“…Because replacement of pk1 with a singlestranded RNA renders tmRNA inactive in the tagging of truncated proteins both in vivo and in vitro, pk1 was suggested to be essential for tmRNA functions (Nameki et al 1999b;Tanner et al 2006). This suggestion is not supported by comparative analyses of tmRNA sequences, which indicate that pk1 is reduced to a single hairpin in some bacterial tmRNAs (Zwieb et al 1999;Gaudin et al 2002;Sharkady and Williams 2004). Moreover, the replacement of pk1 with a stable hairpin yields a mutant tmRNA with nearly wild-type tagging activity (Tanner et al 2006).…”

Variations on the tmRNA gene

“…5,6 The MLR is much more plastic than the TLD; diverse lineages have lost some or all PKs, and in some cases even the tag reading frame. In three bacterial groups, the alphaproteobacteria, some betaproteobacteria, and some cyanobacteria, tmRNA occurs as two RNA chains joined by base-pairing [7][8][9] ( Fig. 1).…”

Evolutionary patterns of non-coding RNAs

“…Usually tmRNA is a single molecule. At least three isolated clades in alphaproteobacteria [197], cyanobacteria [113,437], and beta-proteobacteria [372] have two-component tmRNAs, while jakobids have lost the mRNA-like region in their mitochondrial tmRNAs [179]. Reduction of the tmRNA structure in endosymbionts seems to be a common phenomenon [137].…”