Group II Introns: Structure and Catalytic Versatility of Large Natural Ribozymes

Abstract

Group II introns are large, natural catalytic RNAs or ribozymes that were discovered in organelles of certain protists, fungi, algae, and plants and more recently also in prokaryotic organisms. In vitro, some members were found to self-splice from their pre-RNAs by two consecutive transesterification reactions joining the flanking exons and releasing the intron in a typical lariat form. Apart from self-splicing, a variety of other in vitro activities have been detected for group II introns demonstrating their amazing catalytic versatility. Group II introns fold into a conserved secondary structure consisting of six domains radiating from a central wheel that brings the 5' and 3' splice junction into close proximity. Domain 1 is the largest domain that is assumed to deliver the molecular scaffold assembling the intron in its active structure, while domain 5 is the phylogenetically most conserved part that represents the active site of the ribozyme. In vivo, the splicing reaction of many, if not all group II introns is assisted by proteins either encoded by the introns themselves (maturases), or encoded by other genes of the host organisms. The host proteins known to date have additional cellular functions and seem to have been adapted for splicing during evolution. Some of the protein-encoding group II introns were also shown to act as mobile genetic elements. They can integrate efficiently into intronless alleles of the same gene (homing) and at much lower frequencies into ectopic sites (transposition). The mobility process depends on intron encoded protein functions (endonuclease and reverse transcriptase) and on the intron RNA. This review provides a comprehensive survey of the structure/function relationships and the reaction potential of group II introns, the structurally most complicated, but also most fascinating ribozymes when looking at their catalytic repertoire in vitro and in vivo.

Protein-free small nuclear RNAs catalyze a two-step splicing reaction

“…The first step of splicing in this reaction apparently proceeds through hydrolysis rather than branching; however, catalysis of the first step of splicing through hydrolysis is widely observed in group II introns as a physiological alternative to branching both in vitro and in vivo (29,30). Indeed, under the conditions used in our catalytic assays, hydrolysis is the dominant or even the sole reaction pathway for a number of well-studied introns that can efficiently perform branching in the presence of higher salt concentrations (1,2). Recently, it has been shown that the spliceosomal active site can also catalyze hydrolytic reactions at splice sites by cleavage of the 2nd exon from lariat intermediates or spliced mRNAs (31).…”

Solution Structure of Domain 6 from a Self‐Splicing Group II Intron Ribozyme: A Mg2+ Binding Site is Located Close to the Stacked Branch Adenosine

“…[1] Some group II introns also encode for a maturase protein, enabling these RNAs to act as mobile genetic elements. [1] Although their direct occurrence is nowadays confined to a limited range of organisms, these catalytic RNAs may have played an important role in evolution. Taking into account related nuclear introns and transposable LINE elements, as much as one third of the human DNA may have evolved from ancestral group II introns.…”

“…[2] In addition, based on reaction pathway and sequence similarity, a common ancestry with the eukaryotic spliceosomal machinery has been proposed. [1] The spliceosome is a multicomponent RNA-protein complex that occurs in higher eukaryotes and consists of five highly structured snRNAs (U1, U2, U4, U5 and U6) and numerous proteins, the latter ones presumably having structural roles. [3,4] Here, splicing occurs through the assembly of the snRNAs at pre-mRNA splice sites thereby exhibiting a mechanism that is very similar to the one found for group II introns.…”

Metal ion-N7 coordination in a ribozyme branch domain by NMR

“…the 2'-OH of a conserved adenosine, of these selfsplicing ribozymes, which exhibit a pathway strongly resembling the one of the 3 spliceosomal machinery. [18][19][20] Like all large ribozymes investigated to date, group II introns are obligate metalloribozymes that require Mg 2+ for folding and catalysis. [21][22][23][24][25][26][27] A recent crystal structure of a group IIC intron from Oceanobacillus iheyensis depicts the global architecture although domain 6 is disordered in the crystal.…”