NEW LOOP-LOOP TERTIARY INTERACTIONS IN SELF-SPLICING INTRONS OF SUBGROUP IC AND ID - A COMPLETE 3D MODEL OF THE TETRAHYMENA-THERMOPHILA RIBOZYME

Background: Group I introns self-splice via two consecutive trans-este rification reactions in the presence of guanosine cofactor and magnesi um ions. Comparative sequence analysis has established that a catalyti c core of about 120 nucleotides is conserved in all known group I intr ons. This Gore is generally not sufficient for activity, however, and most self-splicing group I introns require nonconserved peripheral ele ments to stabilize the complete three-dimensional (3D) structure. The physico-chemical properties of group I introns make them excellent sys tems for unraveling the structural basis of the RNA-RNA interactions r esponsible for promoting the self-assembly of complex RNAs. Results: W e present phylogenetic and experimental evidence for the existence of three additional tertiary base pairings between hairpin loops within p eripheral components of subgroup IC1 and ID introns. Each of these new long range interactions, called P13, P14 and P16, involves a terminal loop located in domain 2. Although domains 2 of IC and ID introns sha re very strong sequence similarity, their terminal loops interact with domains 5 and 9 (subgroup IC1) and domain 6 (subgroup ID). Based on t hese tertiary contacts, comparative sequence analysis, and published e xperimental results such as Fe(II)-EDTA protection patterns, we propos e 3D models for two entire group I introns, the subgroup ICI intron in the large ribosomal precursor RNA of Tetrahymena thermophila and the SdCob.1 subgroup ID intron found in the cytochrome b gene of Saccharom yces douglasii. Conclusions: Three-dimensional models of group I intro ns belonging to four different subgroups are now available. They all e mphasize the modular and hierarchical organization of the architecture of group I introns and the widespread use of base-pairings between te rminal hairpin loops for stabilizing the folded and active structures of large and complex RNA molecules. (C) Current Biology Ltd.