Published online 20 April 2005
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Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup
State Key Laboratory of Virology and Department of Biotechnology, College of Life Sciences, Wuhan University Wuhan, Hubei 430072, China
*To whom correspondence should be addressed. Tel: +86 27 68756207; Fax: +86 27 68754945; Email: yizhang{at}whu.edu.cn
Received November 29, 2004. Revised February 26, 2005. Accepted March 29, 2005.
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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