title: Evidence of natural selection to maintain a functional domain outside of the 'core' in a large subclass of group I introns.
abstract: Comparison of three closely-related, homologous Group I introns reveals conservation of RNA secondary structure and some primary sequence outside of the characteristic Group I core structure. Further examination of forty Group I introns showed that all can be placed into one of two categories based on the length of the "loop L5" region (subtended by the base-paired sequences P and Q): short (21 to 38 bases) or long (59 to 295 bases). Despite the large variation in size and sequence, all nineteen of the long L5 introns share a common structure whose features include an adenine-rich bulge at a fixed distance from the P-Q pairing. This bulge is flanked by base-paired regions of greater than or equal to 6 base pairs on the core-proximal side and greater than or equal to 3 base pairs on the distal side. In the core-proximal helix there are a large number and high proportion of deviations from the consensus sequence that maintain base-pairing. These naturally-occurring compensatory base substitutions provide compelling phylogenetic support for the existence of this pairing and indicate that the conserved structure has a function in vivo.
mesh_terms: D001230:Aspergillus / Q000235:genetics; D005075:Biological Evolution; D003576:Electron Transport Complex IV / Q000235:genetics*; D006860:Hydrogen Bonding; D007438:Introns; D009491:Neurospora / Q000235:genetics; D009690:Nucleic Acid Conformation; D012313:RNA; D012326:RNA Splicing; D012335:RNA, Ribosomal / Q000235:genetics; D012568:Schizosaccharomyces / Q000235:genetics
chemical_list: D012335:RNA, Ribosomal; D012313:RNA; D003576:Electron Transport Complex IV