Saito R, Ozawa Y, Kuzuno N, Tomita M
Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center and Genome Science Laboratory, RIKEN Tsukuba Institute Koyadai 3-1-1, Tsukuba Ibaraki 305-0074, Japan.
Gene. 2000 Dec 23;259(1-2):217-22. doi: 10.1016/s0378-1119(00)00429-7.
The processing of 16S rRNA and 23S rRNA by RNase III in E.coli is known to involve stem structures formed by both ends of the rRNA. Indeed, complementary nucleotide sequences are usually found at both ends of 16S rRNA and 23S rRNA. However, whether or not this phenomenon exists in various other bacteria has not yet been adequately studied. We have conducted computer analyses of potential stem structures of rRNA operons in 12 bacterial and 3 archaeal genomes, and compared characteristics of the stem structures among these species. We systematically computed free energy values by exhaustively 'annealing' sequences around the 5' end and sequences around the 3' end of both 16S rRNA and 23S rRNA genes, in order to predict potential stem structures. The results suggest that rRNAs in most species form stem structures at both ends. Some species, such as A.aeolicus, seem to form unusually stable stem structures. On the other hand, some rRNAs, such as rRNAs of D.radiodurans, seem not to form solid stem structures. This suggests that rRNA processing in those species must employ a reliable targeting mechanism other than recognizing stem structures by RNase III.
已知大肠杆菌中核糖核酸酶III对16S核糖体RNA和23S核糖体RNA的加工涉及由核糖体RNA两端形成的茎结构。实际上，在16S核糖体RNA和23S核糖体RNA的两端通常都能发现互补核苷酸序列。然而，这种现象在其他各种细菌中是否存在尚未得到充分研究。我们对12种细菌和3种古细菌基因组中的核糖体RNA操纵子的潜在茎结构进行了计算机分析，并比较了这些物种之间茎结构的特征。为了预测潜在的茎结构，我们通过详尽地“退火”16S核糖体RNA和23S核糖体RNA基因5'端周围的序列以及3'端周围的序列，系统地计算了自由能值。结果表明，大多数物种的核糖体RNA在两端都形成茎结构。一些物种，如嗜热栖热菌，似乎形成了异常稳定的茎结构。另一方面，一些核糖体RNA，如耐辐射球菌的核糖体RNA，似乎没有形成坚实的茎结构。这表明这些物种中的核糖体RNA加工必须采用一种可靠的靶向机制，而不是通过核糖核酸酶III识别茎结构。
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