Zhao Tingting, Zhang Ren, Wang Mingbo
The Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, Jiangsu Province, China.
J Biomed Res. 2010 Jan;24(1):33-42. doi: 10.1016/S1674-8301(10)60006-1.
Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs (sRNAs), some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base pairs. Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes.
具有重要调控作用的小非编码RNA并不局限于真核生物。最近的研究发现了越来越多的细菌小RNA（sRNA），其中一些已被证明可调控关键的细胞过程。计算方法与分子实验相结合，在这些sRNA的鉴定中发挥了重要作用。目前，关于根癌土壤杆菌基因组中是否存在小非编码RNA及其基因尚无相关信息。为了鉴定这种重要细菌中的潜在sRNA，对从根癌土壤杆菌C58中分离的短RNA群体进行了深度测序。从一个包含一万多个短序列的数据集中，基于计算分析初步鉴定出16个候选sRNA。通过RNA折叠预测，所有这些候选序列都能形成茎环结构，并且大多数二级结构富含GC碱基对。有些后面跟着一小段U残基，这表明是不依赖ρ因子的转录终止子，而有些短RNA则位于发夹结构的茎区，这表明是类似真核生物的sRNA。需要使用实验策略来验证这些候选序列。对根癌土壤杆菌中更多候选sRNA的研究将有助于更全面地了解调控RNA在原核生物中的作用范围。
