Open Access Highly Accessed Open Badges Research article

Utilization of tmRNA sequences for bacterial identification

Wilhelm Schönhuber14, Guenhael Le Bourhis23, Josselyne Tremblay2, Rudolf Amann4 and Saulius Kulakauskas2*

Author affiliations

1 Lehrstuhl für Mikrobielle Ökologie, Universität Konstanz, Fach M654, Universitätsstrasse 10, D-78457 Konstanz, Germany

2 Unité de Recherches Laitières et de Génétique Appliquée, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas, France

3 Laboratoire de Pharmacologie des Agents Anticancéreux, Institut Bergonié, 229, Cours de l'Argonne, 33076 Bordeaux, France

4 Max-Planck-Institut für Marine Mikrobiologie, Celsiusstrasse 1, D-28359 Bremen, Germany

For all author emails, please log on.

Citation and License

BMC Microbiology 2001, 1:20  doi:10.1186/1471-2180-1-20

Published: 7 September 2001



Ribosomal RNA molecules are widely used for phylogenetic and in situ identification of bacteria. Nevertheless, their use to distinguish microorganisms within a species is often restricted by the high degree of sequence conservation and limited probe accessibility to the target in fluorescence in situ hybridization (FISH). To overcome these limitations, we examined the use of tmRNA for in situ identification. In E. coli, this stable 363 nucleotides long RNA is encoded by the ssrA gene, which is involved in the degradation of truncated proteins.


Conserved sequences at the 5'- and 3'-ends of tmRNA genes were used to design universal primers that could amplify the internal part of ssrA from Gram-positive bacteria having low G+C content, i.e. genera Bacillus, Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, Listeria, Streptococcus and Staphylococcus. Sequence analysis of tmRNAs showed that this molecule can be used for phylogenetic assignment of bacteria. Compared to 16S rRNA, the tmRNA nucleotide sequences of some bacteria, for example Listeria, display considerable divergence between species. Using E. coli as an example, we have shown that bacteria can be specifically visualized by FISH with tmRNA targeted probes.


Features of tmRNA, including its presence in phylogenetically distant bacteria, conserved regions at gene extremities and a potential to serve as target for FISH, make this molecule a possible candidate for identification of bacteria.