Sugahara Junichi, Kikuta Kaoru, Fujishima Kosuke, Yachie Nozomu, Tomita Masaru, Kanai Akio
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
Mol Biol Evol. 2008 Dec;25(12):2709-16. doi: 10.1093/molbev/msn216. Epub 2008 Oct 1.
The analysis of archaeal tRNA genes is becoming more important to evaluate the origin and evolution of tRNA molecule. Even with the recent accumulation of complete genomes of numerous archaeal species, several tRNA genes are still required for a full complement of the codon table. We conducted comprehensive screening of tRNA genes from 47 archaeal genomes by using a combination of different types of tRNA prediction programs and extracted a total of 2,143 reliable tRNA gene candidates including 437 intron-containing tRNA genes, which covered more than 99.9% of the codon tables in Archaea. Previously, the content of intron-containing tRNA genes in Archaea was estimated to be approximately 15% of the whole tRNA genes, and most of the introns were known to be located at canonical positions (nucleotide position between 37 and 38) of precursor tRNA (pre-tRNA). Surprisingly, we observed marked enrichment of tRNA introns in five species of the archaeal order Thermoproteales; about 70% of tRNA gene candidates were found to be intron-containing tRNA genes, half of which contained multiple introns, and the introns were located at various noncanonical positions. Sequence similarity analysis revealed that approximately half of the tRNA introns found at Thermoproteales-specific intron locations were highly conserved among several tRNA genes. Intriguingly, identical tRNA intron sequences were found within different types of tRNA genes that completely lacked exon sequence similarity, suggesting that the tRNA introns in Thermoproteales could have been gained via intron insertion events at a later stage of tRNA evolution. Moreover, although the CCA sequence at the 3' terminal of pre-tRNA is added by a CCA-adding enzyme after gene transcription in Archaea, most of the tRNA genes containing highly conserved introns already encode the CCA sequence at their 3' terminal. Based on these results, we propose possible models explaining the rapid increase of tRNA introns as a result of intron insertion events via retrotransposition of pre-tRNAs. The sequences and secondary structures of the tRNA genes and their bulge-helix-bulge motifs were registered in SPLITSdb (http://splits.iab.keio.ac.jp/splitsdb/), a novel and comprehensive database for archaeal tRNA genes.
对古菌tRNA基因的分析对于评估tRNA分子的起源和进化变得越来越重要。即使最近众多古菌物种的完整基因组有所积累，但密码子表的完整补充仍需要几个tRNA基因。我们通过结合不同类型的tRNA预测程序，对47个古菌基因组中的tRNA基因进行了全面筛选，共提取了2143个可靠的tRNA基因候选序列，其中包括437个含内含子的tRNA基因，这些基因覆盖了古菌中超过99.9%的密码子表。此前，古菌中含内含子的tRNA基因的含量估计约为整个tRNA基因的15%，并且已知大多数内含子位于前体tRNA（pre-tRNA）的规范位置（核苷酸位置在37和38之间）。令人惊讶的是，我们在嗜热栖热菌目（Thermoproteales）的五个物种中观察到tRNA内含子显著富集；约70%的tRNA基因候选序列被发现是含内含子的tRNA基因，其中一半包含多个内含子，并且这些内含子位于各种非规范位置。序列相似性分析表明，在嗜热栖热菌目特有的内含子位置发现的tRNA内含子中，约一半在几个tRNA基因中高度保守。有趣的是，在完全缺乏外显子序列相似性的不同类型的tRNA基因中发现了相同的tRNA内含子序列，这表明嗜热栖热菌目中的tRNA内含子可能是在tRNA进化的后期通过内含子插入事件获得的。此外，尽管古菌中pre-tRNA 3'末端的CCA序列在基因转录后由CCA添加酶添加，但大多数含有高度保守内含子的tRNA基因在其3'末端已经编码了CCA序列。基于这些结果，我们提出了可能的模型来解释由于pre-tRNA的逆转录转座导致的内含子插入事件而使tRNA内含子快速增加的现象。tRNA基因的序列和二级结构及其凸起-螺旋-凸起基序已登记在SPLITSdb（http://splits.iab.keio.ac.jp/splitsdb/）中，这是一个用于古菌tRNA基因的新颖且全面的数据库。
