Watanabe Yoh-ichi, Kawarabayasi Yutaka
University of Tokyo, Graduate School of Medicine, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
Kyushu University, Faculty of Agriculture, Hakozaki 6-10-1, Fukuoka 812-8581, Japan.
Int J Mol Sci. 2015 Jan 20;16(1):2187-203. doi: 10.3390/ijms16012187.
Based on the genomic sequences for most archaeal species, only one tRNA gene (isodecoder) is predicted for each triplet codon. This observation promotes analysis of a whole set of tRNA molecules and actual splicing patterns of interrupted tRNA in one organism. The entire genomic sequences of two Creanarchaeota, Aeropyrum pernix and Sulfolobus tokodaii, were determined approximately 15 years ago. In these genome datasets, 47 and 46 tRNA genes were detected, respectively. Among them, 14 and 24 genes, respectively, were predicted to be interrupted tRNA genes. To confirm the actual transcription of these predicted tRNA genes and identify the actual splicing patterns of the predicted interrupted tRNA molecules, RNA samples were prepared from each archaeal species and used to synthesize cDNA molecules with tRNA sequence-specific primers. Comparison of the nucleotide sequences of cDNA clones representing unspliced and spliced forms of interrupted tRNA molecules indicated that some introns were located at positions other than one base 3' from anticodon region and that bulge-helix-bulge structures were detected around the actual splicing sites in each interrupted tRNA molecule. Whole-set analyses of tRNA molecules revealed that the archaeal tRNA splicing mechanism may be essential for efficient splicing of all tRNAs produced from interrupted tRNA genes in these archaea.
基于大多数古菌物种的基因组序列，每个三联体密码子预计只有一个tRNA基因（同功tRNA）。这一观察结果有助于对一个生物体中的整套tRNA分子以及中断型tRNA的实际剪接模式进行分析。大约15年前测定了两种泉古菌——嗜热栖热菌和硫磺矿硫化叶菌的完整基因组序列。在这些基因组数据集中，分别检测到47个和46个tRNA基因。其中，分别有14个和24个基因被预测为中断型tRNA基因。为了证实这些预测的tRNA基因的实际转录情况，并确定预测的中断型tRNA分子的实际剪接模式，从每种古菌物种中制备了RNA样本，并用于用tRNA序列特异性引物合成cDNA分子。对代表中断型tRNA分子未剪接和剪接形式的cDNA克隆的核苷酸序列进行比较表明，一些内含子位于反密码子区域3'端一个碱基以外的位置，并且在每个中断型tRNA分子的实际剪接位点周围检测到凸起-螺旋-凸起结构。对tRNA分子的全组分析表明，古菌tRNA剪接机制对于这些古菌中由中断型tRNA基因产生的所有tRNA的有效剪接可能至关重要。
