title: Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup.
abstract: 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.
authors.affiliation: State Key Laboratory of Virology and Department of Biotechnology, College of Life Sciences, Wuhan University Wuhan, Hubei 430072, China.
authors.forename: Zhijie
authors.initials: Z
authors.lastname: Li
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D014644:Genetic Variation; D007438:Introns; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D016337:RNA, Catalytic / Q000737:chemistry* / Q000145:classification; D017423:Sequence Analysis, RNA
chemical_list: D016337:RNA, Catalytic