Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns

Both Group I and Group II intron RNAs are capable of self splicing, with cleavage-ligation proceeding by concerted transesterification reactions. Although they tend to be localized to the same cellular compartments (mitochondria and chloroplasts), these two categories of self-splicing RNAs bear no features that would indicate a common evolutionary origin. Recent attempts to ascribe similarities to the intermolecular structures formed in nuclear spliceosomes and the intramolecular structures in group I and group II introns underscore the current interest in determining the evolutionary origins and interactions of these self-splicing intron classes. These introns commonly contain open reading frames (ORFs) that are closely related within, but not between, groups. Many group I ORFs encode endonucleases. Two major families have been identified, characterized by dodecapeptide (also called LAGLI-DADG) and GIY-YIG motifs, respectively. However, many other group I endonucleases have no known relatives. Of the group II introns that have sizeable ORFs, many (24 of 34 in a recent compilation) bear extensive similarity to reverse transcriptases, and half of those also have a 'zinc-finger-like' motif at their carboxyl termini. While using BLAST to identify conserved amino acid sequences in group I ORFs with no known relatives, we were surprised to encounter a relatively significant match (score = 64; Poisson probability, P = 0.010) between a segment of the nrdB intron endonuclease (I-TevIII) of the T4-like phage RB3, and a zinc-finger-like domain from the cyanobacterial group II intron Cal.x2. Interestingly, although two zinc fingers had previously been identified near the carboxyl terminus of I-TevIII (Refs 9, 11), the segment identified in this alignment is near the I-TevIII amino terminus, and does not have all the features of a zinc finger. (DBO)