| Group â… introns are a class of catalytic RNAs, which are capable of catalyzing their own excision from the precursor RNAs by a two-step phosphodiester transfer reaction. Previous study had proved that the group I introns need to be folded into defined structures to carry out the catalytic activity. Although having great variance in sequence, group I introns share a number of conserved base-paired regions, which take part in the formation of the catalytic structure. However, the highly variable sequence and presence of a pseudoknot in their core sequences preclude the attempts for predicting their native secondary structures by currently available computer algorisms.In this work, we have predicted secondary structures for the currently known 211 introns in the subgroup E mainly by using a manual strategy. Based on the secondary structure predictions, we were able to produce reliable sequence alignments for the 211 introns. By examining the alignments, we were able to identify 14 conserved base-paired segments, which include 5 characteristic base-paired segments besides the 9 conserved over all group I introns. 4 out of the 5 characteristic base-paired segements were local base pairings, namely P2, P2.1, P9.1 and P9.2. The other one, P13, was a long-range base-paired segment between the terminal loops of P2.1 and P9.1. The conbination of the long-range base-pairings (P3, P7, P10 and P13) in subgroup E introns, actually made the introns into higher order pseudoknots. An interesting phenomenon was also noticed, that between the local and long-range base-paired regions, competing base pairings are found in significant dominance of all introns. This sheds light on the strategy employed by complex RNAs in establishing long-range base-paired segments in the folding process. We found characteristic structural motifs in these introns, including the green algal SSU 516 introns' expanded GNRA loops resided in their P9 and P9.2 terminal loop, the P6 GYNRCG terminal loop and branched P2.1ab in SSU 989 and SSU 1199 introns, the prevalent bulged-A in P3, P6 and P2.1 stems. These findings would lead to further understanding in the building of the three dimensional structure of subgroup E introns.A distance analysis of core sequences of these introns revealed three clusters existing in the subgroup E. Statistic of the peripheral secondary structure motifs support the hypothesis of existence of intron lineages in some groups of introns. As to the origin and phylogeny of these introns, we found the introns from the same insertion site and same genus always share high degree of structural similarity, which suggests stable inheritance within host genes. However, introns with high degree of homology were found in distantly related hosts, which provide direct evidences for early lateral transfer of introns among different host species. On the other hand, the homology between the exon sequences and the similarity of the inserted introns in the SSU 989 and SSU 1199 sites strongly suggest common ancestor of these introns and early lateral transfers among homologous rRNA sites.Accordingly, we found although most group IE introns are too short to code for homing endonucleases, 4 long introns do contain the characteristic His-Cys boxes for homing endonucleases. And 3 of them were newly found in this study. Hence we propose that besides the predominant stable inherited introns, some introns might still be possessing lateral transfer capabilities. And lateral transfers should have been responsible for the early spread out of group IE introns to a broad range of hosts.
|
PDF Full Text Request