Utilization of tmRNA sequences for bacterial identification.
Utilization of tmRNA sequences for bacterial identification.
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DOI：
10.1186/1471-2180-1-20
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发表时间：
2001-09-07
期刊：
影响因子：
4.2
通讯作者：
Kulakauskas, S
中科院分区：
文献类型：
--
作者：
Schonhuber, W;Le Bourhis, G;Kulakauskas, S
背景：核糖体RNA分子被广泛用于细菌的系统发育和原位鉴定。然而，它们用于区分物种内的微生物通常受到高度序列保守性和荧光原位杂交（FISH）中探针对靶标的有限可及性的限制。为了克服这些局限性，我们研究了使用tmRNA原位鉴定。在大肠在大肠杆菌中，ssrA基因编码的363个核苷酸长的稳定RNA参与了截短蛋白的降解。利用tmRNA基因5 ′-和3 ′-末端的保守序列设计通用引物，该通用引物可以扩增来自具有低G+C含量的革兰氏阳性菌，即芽孢杆菌属、肠球菌属、乳球菌属、乳杆菌属、明串珠菌属、李斯特菌属、链球菌和葡萄球菌。tmRNAs序列分析表明，该分子可用于细菌的系统发育分配。与16 S rRNA相比，一些细菌（例如李斯特菌）的tmRNA核苷酸序列在物种之间显示出相当大的差异。使用大肠以大肠杆菌为例，我们已经表明，细菌可以特异性地通过FISH与tmRNA靶向probes.CONCLUSIONS：tmRNA的特点，包括它的存在，在基因末端的保守区域和潜在的作为FISH的目标，使这个分子的细菌鉴定的一个可能的候选。
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.