A new nomenclature of group I introns in ribosomal DNA

Abstract

The current nomenclature system of group I introns (see Cech, 1988; Michel & Westhof, 1990) has become insufficient to distinguish and categorize the complex collection of more than 900 group I introns in ribosomal DNA (rDNA) of nuclear, mitochondrial, chloroplast, and eubacterial genomes (http://www.rna.icmb.utexas.edu/; GenBank; our unpubl. results) in a rational way. The majority of these group I introns (∼750) are found in nuclear rDNA of fungi and protists, but the distribution appears highly scattered since most species analyzed lack introns. Many of the rDNA introns are optional among strains of a particular species or between closely related species, and some have been shown in experimental settings to be true mobile genetic elements (see Belfort & Roberts, 1997). All group I rDNA introns are found at a limited number of insertion sites (∼75) in highly conserved regions of the small subunit (SSU) and large subunit (LSU) rRNA genes, and some of these sites (∼10) are shared by introns from the nuclei, mitochondria, or chloroplasts. There are numerous examples of multiple group I introns in a single rRNA gene, and as many as eight nuclear introns have been noted in the SSU rDNA of the lichen ascomycete Lecanora dispersa (accession number L37734) and in the LSU rDNA of the myxomycete Fuligo septica (our unpubl. results). Finally, group I introns that occupy the same site in rDNA, but in distantly related hosts, tend to share a number of structural features as well as high levels of primary sequence similarities compared to introns at different insertion sites (e.g., Suh et al., 1999).