Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup

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.