| Group II Introns
Group II introns are an ancient class of ribozymes that can catalyze a striking diversity of chemical reactions on RNA and DNA. They are large molecules (~450 - 1000 nucleotides) with a distinctive secondary structure and a reactive tertiary structure that forms in the presence of magnesium ions. Group II introns can cut themselves out of a strand of RNA and ligate the pieces back together again. The liberated intron molecules are also highly reactive, and they are capable of targeting and reacting with complementary pieces of RNA and DNA. Through cutting and pasting reactions, free introns can insert themselves into new target sequences, thereby hopping from one genomic location to another within a host, or between species. Thus, group II introns are mobile genetic elements that inhabit and shape the genomes of bacteria, fungi, diverse microeukaryotes, plants and some animals (for reviews, see Pyle, Ribozymes, RSC Publishing, 2008; Pyle & Lambowitz, RNA World Volume 3, 2007; Lehmann & Schmidt, Crit Rev Biochem Mol, 2003).
Although they continue to exert a major influence on the metabolism of these modern organisms, group II introns are also of great historical importance, as they are believed to share a common ancestor with the original introns that proliferated throughout all eukaryotic genomes. By breaking eukaryotic coding sequences into pieces that can rejoin or "splice" in different combinations, group II introns may have enabled eukaryotes to encode hundreds of different proteins within a single gene. By helping us break the "one gene one protein barrier", group II introns may have contributed to the great diversity that we observe in life today. The catalytic machinery for group II intron splicing probably evolved into the eukaryotic "spliceosome", which is the large ribonucleoprotein machine that catalyzes splicing in higher eukaryotes, and which has active-site components that are similar to modern group II introns.
A glimpse of the earliest eukaryotic splicing machine is provided by the high-resolution crystal structure of an intact group IIC intron, which was recently solved by our group (Toor et al, Science 2008). This elaborate structure is a rich trove of new information on RNA structural elements and ribozyme catalytic strategies. The group IIC structure reveals a complex scaffold (comprised of intron Domain 1) that enfolds the active-site, which is comprised of a bulge motif that is integrated within a major-groove triple helix on the surface of intron Domain 5. The resulting structure forms a site for the binding of two divalent metal ions that are spaced 3.9 Å apart, which is the ideal distance for metals that participate directly in phosphodiester cleavage reactions (the classical two-metal ion mechanism). The crystal structure also reveals that structural motifs known to be similar to spliceosomal domains are closely clustered in space, suggesting that the two systems share a common ancestor.
In addition to providing new information on the catalytic mechanism and evolutionary history of group II introns (of which the group IIC class is the most ancient lineage), the crystal structure provides a wealth of new insights into RNA tertiary structure and its component motifs. The active-site itself contains unusual substructures, including the tight turn of the Domain 5 bulge and the remarkable major-groove triplex that supports the metal ion binding site. The five-way junction of the Domain 1 scaffold is an extraordinarily complex assembly of interdigitated motifs and intercalated stacking arrays. The z-anchor motif that helps D1 dock with D5 contains an unusual base quartet and a base-triple that is exactly as predicted from previous chemogenetic work on the structure of group IIB introns. Indeed, the striking agreement between the crystal structure and previous biochemical studies on the ai5γ group IIB intron (including all crosslinks, NAIS constraints and the most recent 3-D model (De Lencastre & Pyle, NSMB 2005; De Lencastre & Pyle, RNA 2007)) indicates that the crystal structure represents an active and biologically relevant form of the intron, and that all group II introns share a very similar core architecture.