PMID- 11560762
OWN - NLM
STAT- MEDLINE
DCOM- 20021202
LR  - 20191105
IS  - 1471-2180 (Electronic)
IS  - 1471-2180 (Linking)
VI  - 1
DP  - 2001 Sep 7
TI  - Utilization of tmRNA sequences for bacterial identification.
PG  - 20
AB  - BACKGROUND: 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. RESULTS: 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. 
      CONCLUSIONS: 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.
FAU - Schonhuber, W
AU  - Schonhuber W
AD  - Lehrstuhl fur Mikrobielle Okologie, Universitat Konstanz, Fach M654, 
      Universitatsstrasse 10, D-78457 Konstanz, Germany. 
      wilhelm.schoenhuber@uni-konstanz.de
FAU - Le Bourhis, G
AU  - Le Bourhis G
FAU - Tremblay, J
AU  - Tremblay J
FAU - Amann, R
AU  - Amann R
FAU - Kulakauskas, S
AU  - Kulakauskas S
LA  - eng
PT  - Journal Article
DEP - 20010907
PL  - England
TA  - BMC Microbiol
JT  - BMC microbiology
JID - 100966981
RN  - 0 (RNA Probes)
RN  - 0 (RNA, Bacterial)
RN  - 0 (RNA, Messenger)
RN  - 0 (tmRNA)
RN  - 9014-25-9 (RNA, Transfer)
SB  - IM
MH  - Bacteria/*genetics/*isolation & purification
MH  - Base Sequence/genetics
MH  - Evolution, Molecular
MH  - Gram-Positive Bacteria/genetics/isolation & purification
MH  - In Situ Hybridization, Fluorescence
MH  - Lactococcus lactis/genetics/isolation & purification
MH  - Phylogeny
MH  - RNA Probes/genetics
MH  - RNA, Bacterial/*genetics
MH  - RNA, Messenger/genetics
MH  - RNA, Transfer/genetics
MH  - Sequence Analysis, RNA
MH  - Species Specificity
PMC - PMC55692
EDAT- 2001/09/19 10:00
MHDA- 2002/12/03 04:00
PMCR- 2001/09/07
CRDT- 2001/09/19 10:00
PHST- 2001/05/21 00:00 [received]
PHST- 2001/09/07 00:00 [accepted]
PHST- 2001/09/19 10:00 [pubmed]
PHST- 2002/12/03 04:00 [medline]
PHST- 2001/09/19 10:00 [entrez]
PHST- 2001/09/07 00:00 [pmc-release]
AID - 1471-2180-1-20 [pii]
AID - 10.1186/1471-2180-1-20 [doi]
PST - epublish
SO  - BMC Microbiol. 2001 Sep 7;1:20. doi: 10.1186/1471-2180-1-20.