Pánek Josef, Bobek Jan, Mikulík Karel, Basler Marek, Vohradský Jirí
Laboratory of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
BMC Genomics. 2008 May 13;9:217. doi: 10.1186/1471-2164-9-217.
The first systematic study of small non-coding RNAs (sRNA, ncRNA) in Streptomyces is presented. Except for a few exceptions, the Streptomyces sRNAs, as well as the sRNAs in other genera of the Actinomyces group, have remained unstudied. This study was based on sequence conservation in intergenic regions of Streptomyces, localization of transcription termination factors, and genomic arrangement of genes flanking the predicted sRNAs.
Thirty-two potential sRNAs in Streptomyces were predicted. Of these, expression of 20 was detected by microarrays and RT-PCR. The prediction was validated by a structure based computational approach. Two predicted sRNAs were found to be terminated by transcription termination factors different from the Rho-independent terminators. One predicted sRNA was identified computationally with high probability as a Streptomyces 6S RNA. Out of the 32 predicted sRNAs, 24 were found to be structurally dissimilar from known sRNAs.
Streptomyces is the largest genus of Actinomyces, whose sRNAs have not been studied. The Actinomyces is a group of bacterial species with unique genomes and phenotypes. Therefore, in Actinomyces, new unique bacterial sRNAs may be identified. The sequence and structural dissimilarity of the predicted Streptomyces sRNAs demonstrated by this study serve as the first evidence of the uniqueness of Actinomyces sRNAs.
首次对链霉菌中的小非编码RNA（sRNA，ncRNA）进行了系统研究。除少数例外，链霉菌的sRNA以及放线菌属其他类群中的sRNA尚未得到研究。本研究基于链霉菌基因间区域的序列保守性、转录终止因子的定位以及预测的sRNA侧翼基因的基因组排列。
预测出链霉菌中32个潜在的sRNA。其中，通过微阵列和RT-PCR检测到20个的表达。通过基于结构的计算方法验证了预测结果。发现两个预测的sRNA由不同于不依赖Rho的终止子的转录终止因子终止。通过计算以高概率鉴定出一个预测的sRNA为链霉菌6S RNA。在32个预测的sRNA中，发现24个在结构上与已知sRNA不同。
链霉菌是放线菌中最大的属，其sRNA尚未得到研究。放线菌是一组具有独特基因组和表型的细菌物种。因此，在放线菌中可能会鉴定出新的独特细菌sRNA。本研究证明的预测链霉菌sRNA的序列和结构差异是放线菌sRNA独特性的首个证据。
