Recurrent insertion of 5′-terminal nucleotides and loss of the branchpoint motif in lineages of group II introns inserted in mitochondrial preribosomal RNAs

Abstract

A survey of sequence databases revealed 10 instances of subgroup IIB1 mitochondrial ribosomal introns with 1 to 33 additional nucleotides inserted between the 59 exon and the consensus sequence at the intron 59 end. These 10 introns depart further from the IIB1 consensus in their predicted domain VI structure: In contrast to its basal helix and distal GNRA terminal loop, the middle part of domain VI is highly variable and lacks the bulging A that serves as the branchpoint in lariat formation. In vitro experiments using two closely related IIB1 members inserted at the same ribosomal RNA site in the basidiomycete fungi Grifola frondosa and Pycnoporellus fulgens revealed that both ribozymes are capable of efficient self-splicing. However, whereas the Grifola intron was excised predominantly as a lariat, the Pycnoporellus intron, which possesses six additional nucleotides at the 59 end, yielded only linear products, consistent with its predicted domain VI structure. Strikingly, all of the introns with 59 terminal insertions lack the EBS2 exon-binding site. Moreover, several of them are part of the small subset of group II introns that encode potentially functional homing endonucleases of the LAGLIDADG family rather than reverse transcriptases. Such coincidences suggest causal relationships between the shift to DNA-based mobility, the loss of one of the two ribozyme sites for binding the 59 exon, and the exclusive use of hydrolysis to initiate splicing.

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

“…2D) (23); and the only group II intron identified so far in large sulfur bacteria was S1396, which belonged to the subgroup IIC (Fig. 2C) (24)(25)(26)(27). Furthermore, S1396 showed parallels to a functional type of group II introns described recently by Li et al (25).…”

“…Furthermore, S1396 showed parallels to a functional type of group II introns described recently by Li et al (25). Special features include the presence of several additional nucleotides inserted at the 5′-end and the possession of a gene for a LAGLIDADG homing endonuclease [which is more commonly found in group I introns (20)] instead of a reverse transcriptase (25), which were traits likewise found in S1396.…”

“…S4) (29,34). Generally, this family of homing endonucleases is encoded by group I introns (20), but can be occasionally found in group II introns (25,35,36). The remaining 35 introns either lacked an ORF or had a truncated ORF.…”

Novel RNA structural features of an alternatively splicing group II intron from Clostridium tetani

“…Apart from the interest in how a mobile group II intron evolved to be an alternatively splicing intron, the changes in C.te.I1 RNA structure and ribozyme properties are intriguing because a very similar set of changes has been observed in mitochondrial rRNA group II introns (Li et al 2011). The similarities suggest that this set of ribozyme adaptations exemplify an inherent dynamic for the evolution of group II introns.…”

“…Another potential adaptation that may promote the shifted splice site is the loss of the IBS2-EBS2 interaction. Although not tested experimentally here, it has been noted that other group II introns that use a shifted 5 ′ splice site have also lost their IBS2-EBS2 motifs (Li et al 2011;see below).…”