Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals aspecific structural signature

Bacterial tmRNA mediates a trans-translation reaction, which permits the re cycling of stalled ribosomes and probably also contributes to the regulated expression of a subset of genes. its action results in the addition of a s mall number of C-terminal amino acids to protein whose synthesis had stalle d and these constitute a proteolytic recognition tag for the degradation of these incompletely synthesized proteins. Previous work has identified pseu doknots and stem-loops that are widely conserved in divergent bacteria, In the present work an alignment of tmRNA gene sequences within 13 beta -prote obacteria reveals an additional sub-structure specific for this bacterial g roup. This sub-structure is in pseudoknot Pk2, and consists of one to two a dditional stem-loop(s) capped by stable GNRA tetraloop(s), Three-dimensiona l models of tmRNA pseudoknot 2 (Pk2) containing various topological version s of the additional substructure suggest that the sub-structures likely poi nt away from the core of the RNA, containing both the tRNA and the mRNA dom ains. A putative tertiary interaction has also been identified.