Group II introns: structure, folding and splicing mechanism

Abstract

Group II introns are large autocatalytic RNAs found in organellar genomes of plants and lower eukaryotes, as well as in some bacterial genomes. Interestingly, these ribozymes share characteristic traits with both spliceosomal introns and non-LTR retrotransposons and may have a common evolutionary ancestor. Furthermore, group II intron features such as structure, folding and catalytic mechanism differ considerably from those of other large ribozymes, making group II introns an attractive model system to gain novel insights into RNA biology and biochemistry. This review explores recent advances in the structural and mechanistic characterization of group II intron architecture and self-splicing.

Influence of decreased solvent permittivity on the structure and magnesium(II)-binding properties of the catalytic domain 5 of a group II intron ribozyme

“…Indeed, D5 is embedded within the innermost core of the ribozyme architecture undergoing numerous tertiary contacts, i.e. the λ-λ', κ-κ', μ-μ', ψ-ψ', and ζ-ζ' interactions with D1 and D3 [2]. The conserved bulge thereby plays a crucial role and it is well feasible that the tertiary interactions are formed by a concerted action of the formation of hydrogen bonds and reduced permittivity upon assembly of the catalytic core.…”

“…Group II introns are large metallo-ribozymes with a size ranging between 600 and 2500 nucleotides that were discovered in protists, fungi, algae, and plants as well as in some prokaryotic organisms [1,2]. These large molecular machines are self-splicing introns catalyzing their own removal from the pre-RNA initially formed during transcription.…”

“…In contrast to the spliceosome, group II introns show a larger variety of reactions, e.g. these ribozymes are capable of reinserting themselves into RNA or DNA, thus rendering them mobile genetic elements [1,2,4]. All group II introns possess a conserved secondary structure consisting of six domains, which all have specific functions for folding and catalysis.…”

“…Unlike the other domains, domain 5 (D5) is highly conserved in sequence and length. It forms a very stable hairpin of mostly 34 nucleotides and represents the most essential active-site part of all group II introns [1,2]. It is remarkable that the individual domains of group II introns are independent folding units that reassemble to the full active structure when added in trans to each other [2,5].…”

“…It forms a very stable hairpin of mostly 34 nucleotides and represents the most essential active-site part of all group II introns [1,2]. It is remarkable that the individual domains of group II introns are independent folding units that reassemble to the full active structure when added in trans to each other [2,5]. It has been shown that metal ions thereby occupy the same sites in the free domains as well as in the assembled three dimensional architecture of the fully functional ribozyme [6].…”