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.

Toward predicting self-splicing and protein-facilitated splicing of group I introns

“…For example, the S.d. intron (which possesses a L9-P5 interaction but no L2-P8 interaction) is poised for catalysis by subgroup IE-specific interactions involving the P3, P2.1, and P6 helices, which all adopt the consensus sequence observed for these helices (Li and Zhang 2005). Overall, these results further support the notion that long range interactions between peripheral elements are key determinants of the ability of group I introns to self-splice.…”

“…c Based on the classification by Michel and Westhof (1990), expanded by Suh et al (1999) and Li and Zhang (2005 efficient self-splicing (Table 1). Data for 26 other group I introns described in the literature generally support this criterion and revealed a correlation to the difference between the GC content of an intron and that of its host genome (Supplemental material), as follows.…”

“…Tertiary interactions were also proposed at the periphery, for example, involving the tetraloop L9 and either two consecutive base pairs or an 11-nt receptor in P5 (an L9-P5 interaction is almost universally found in group I introns; Michel and Westhof 1990;Costa and Michel 1995;Hammann and Westhof 2007) or involving L2 and P8 in a similar interaction, which plays a critical role in properly positioning the P1-P2 substrate domain in the catalytic site (Michel and Westhof 1990;Costa and Michel 1995;Jaeger et al 1996). Subgroup-specific interactions, such as the triple-helical interaction involving P6, P2.1, and P3 in subgroup IE introns (Li and Zhang 2005), were compiled as well. Additionally, the sarcin/ricin motif (Leontis and Westhof 1998;Leontis et al 2002) was modeled in peripheral regions when the consensus sequence was detected (e.g., in P7.1 of C.b.…”

“…Group I introns possess at their core a conserved architecture formed by 10 paired segments (P1-P10) organized in three domains: a structural domain (P4-P6) that folds independently in the Tetrahymena rRNA intron (Murphy and Cech 1993), a substrate domain (P1, P10), and a catalytic domain (P3, P7, and P8) (Michel and Westhof 1990;Golden et al 1998). These introns are classified into 14 subgroups (IA1-3, IB1-4, IC1-3, ID, IE1-3) based on conservation of the core domains and on the presence of characteristic peripheral elements (e.g., P2, P7.1, P7.2, and P9) (Michel and Westhof 1990;Lehnert et al 1996;Suh et al 1999;Li and Zhang 2005). In general, the peripheral elements form long-range tertiary interactions that stabilize the core domains to promote catalysis (Jaeger et al 1991;Costa and Michel 1995;Lehnert et al 1996).…”

Photobiont Flexibility in <i>Paramecium bursaria</i>: Double and Triple Photobiont Co-Habitation

“…Due to the intron spreading mechanisms, IE introns have strong insertion bias to limited positions. In green algae, nearly all IE introns are located at S516 (S = SSU rRNA; the numbering reflects their homologous position in the Escherichia coli rRNA gene) [20,23]. However, four (S943, L1688, L2184, and L2449; L = LSU rRNA) out of six introns of P. bursaria photobionts occupied novel insertion sites.…”