Introns in organelle genomes demonstrate wide variation in both features and behavior in Nature. Three classes of organelle introns are now recognized: 1) Group I, 2) Group II, and 3) Group III which are related to Group II introns. These introns have attracted considerable attention because of two remarkable properties: 1) the ability to self-splice, 2) the ability to function as mobile elements. These properties are being explored in order to understand gene evolution and as potential tools in genetic engineering and genomic analysis.

Characteristics of Group I, Group II and III Introns

Group I introns Group I introns are ribozymes with distinctive secondary structures containing a conserved catalytic center of paired regions 1-9, but no splice site consensus. Splicing of group I introns is by sequential transesterifications with external guanosine as initiating nucleophile for the first step. The linear excised intron is subsequently circularized. Group I introns are present in rRNA, tRNA, and protein-coding genes. They are particularly abundant in fungal and some plant mitochondrial DNAs, chloroplast DNA in Chlamydomonas spp., but also in nuclear rRNA genes of Tetrahymena and other lower eukaryotes, in bacteriophage, and in several tRNA genes in eubacteria. Many introns studied to date are able to self-splice, but protein machinery is probably required in vivo. Group II introns Group II introns also are ribozymes with distinctive secondary structures (domains I-VI), with a catalytic center formed by domain I (dI) and dV. They have conserved 5'- and 3'- boundary sequences (GUGYG and AY respectively). Splicing of group II introns is by a two transesterification reactions with a dVI bulged adenosine as initiating nucleophile; the intron is exercised as a lariat. Two major subclasses of group II introns (IIA and IIB) have been distinguished based on structural features. They are found in rRNA, tRNA, mRNA of organelles in fungi, plants, protists, and mRNA in bacteria. Self-splicing occurs in vitro (for a few of the introns studied to date), but protein machinery is probably required in vivo . Group III introns Group III introns are short group II-like introns found in mRNA genes of chloroplasts in euglenoid protists. They have a conventional group II-type dVI with a bulged adenosine, a streamlined dI, no dII-dV, and a relaxed splice site consensus. Splicing is by two transesterification reactions with a dVI bulged adenosine as initiating nulceophile; the intron is exercised as a lariat.

FUGOID collects and integrates various structural and functional data on organellar (mitochondrial and chloroplast) introns, particularly functional information about intron splicing and mobility. It is implemented in a relational database management system and can be searched either by intron information or by a major reference. Data entry and revision systems have also been developed. In order to submit or update data directly on the web, please contact herrin@mail.utexas.edu .