Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup.
Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup.
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DOI：
10.1093/nar/gki517
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发表时间：
2005
影响因子：
14.9
通讯作者：
Zhang Y
中科院分区：
文献类型：
--
作者：
Li Z;Zhang Y
目前公共数据库中大量可用的I组内含子序列为通过大规模比较序列分析来研究这一结构复杂的催化RNA大家族提供了机会。在这项研究中，人工预测了IE亚群中211个I组内含子的详细二级结构。二级结构有利的比对表明，IE内含子含有14个保守的茎。P2.1和P9.1之间通过长距离碱基配对形成的P13茎在IE内含子中保守。保守核心中的序列变异将IE内含子分为三个不同的子亚群，即IE1、IE2和IE3。外围结构基序与核心序列的协变支持外围元件在核心结构折叠中的辅助作用。有趣的是，在插入在S516位置的IE2内含子中发现了宿主特有的结构基序。竞争性碱基配对在所有长程配对区域的连接处被发现是保守的，这表明在大RNA折叠过程中建立长程碱基配对的可能机制。这些发现扩展了我们对IE内含子的认识，表明比较分析可以很好地补充我们对基因组时代RNA结构和功能的理解。
The large number of currently available group I intron sequences in the public databases provides opportunity for studying this large family of structurally complex catalytic RNA by large-scale comparative sequence analysis. In this study, the detailed secondary structures of 211 group I introns in the IE subgroup were manually predicted. The secondary structure-favored alignments showed that IE introns contain 14 conserved stems. The P13 stem formed by long-range base-pairing between P2.1 and P9.1 is conserved among IE introns. Sequence variations in the conserved core divide IE introns into three distinct minor subgroups, namely IE1, IE2 and IE3. Co-variation of the peripheral structural motifs with core sequences supports that the peripheral elements function in assisting the core structure folding. Interestingly, host-specific structural motifs were found in IE2 introns inserted at S516 position. Competitive base-pairing is found to be conserved at the junctions of all long-range paired regions, suggesting a possible mechanism of establishing long-range base-pairing during large RNA folding. These findings extend our knowledge of IE introns, indicating that comparative analysis can be a very good complement for deepening our understanding of RNA structure and function in the genomic era.
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