Comprehensive Analysis of Archaeal tRNA Genes Reveals Rapid Increase of tRNA Introns in the Order Thermoproteales
Comprehensive Analysis of Archaeal tRNA Genes Reveals Rapid Increase of tRNA Introns in the Order Thermoproteales
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DOI：
10.1093/molbev/msn216
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发表时间：
2008-12-01
影响因子：
10.7
通讯作者：
Kanai, Akio
中科院分区：
文献类型：
--
作者：
Sugahara, Junichi;Kikuta, Kaoru;Kanai, Akio
对古生菌tRNA基因的分析对于评价tRNA分子的起源和进化变得越来越重要。即使最近积累了许多古生菌物种的完整基因组，但仍需要几个tRNA基因才能完全补充密码子表。我们结合不同类型的tRNA预测程序对47个古生菌基因组中的tRNA基因进行了全面的筛选，共提取了2143个可靠的tRNA基因候选，其中包含437个内含子的tRNA基因，覆盖了古生代99.9%以上的密码子表。此前，含内含子的tRNA基因在古生物中的含量估计约占整个tRNA基因的15%，并且大多数内含子位于前体tRNA(Pre-tRNA)的典型位置(核苷酸位置在37-38之间)。令人惊讶的是，我们观察到在古生目ThermoProteales的五种物种中tRNA内含子显著丰富；大约70%的tRNA基因候选被发现是含有内含子的tRNA基因，其中一半含有多个内含子，内含子位于不同的非规范位置。序列相似性分析表明，在ThermoProteales特异内含子位置发现的tRNA内含子中，约有一半在几个tRNA基因之间高度保守。有趣的是，在不同类型的tRNA基因中发现了完全缺乏外显子序列相似性的相同tRNA内含子序列，这表明ThermoProteales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，虽然在古生代中，前tRNA 3‘端的CCA序列是在基因转录后被CCA添加酶添加的，但大多数含有高度保守内含子的tRNA基因在其3’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，解释了通过前tRNA的逆转录转座导致内含子插入事件导致tRNA内含子快速增加的原因。TRNA基因的序列和二级结构及其凸起-螺旋-凸起基序在SPLITSdb http://splits.iab.keio.ac.jp http://www.w3.org，中注册，SPLITSdb是一个新的全面的古菌tRNA基因数据库。
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 http://www.w3.org, a novel and comprehensive database for archaeal tRNA genes.