Specialized lineages of bacterial group II introns

The Avi.groEL intron of Azotobacter vinelandii, which interrupts the termination codon of the groEL gene, is shown to belong to a monophyletic subset of bacterial group II introns that share a large insertion at their 5′ extremity and a peculiar genetic localization. Some of these introns are inserted within, right next to, or very close to, a stop codon while others are located immediately 3′ of, or close to, an initiation codon. After subgroup IIC introns, which target rho-independent transcription terminators, this is the second instance of a genetically specialized lineage of bacterial group II introns. Both the members of subgroup IIC and the relatives of Avi.groEL stand in contrast against the rest of group II retrotransposons in that features other than sequence must be used in target recognition. Among other specialized characters that could unite the two subgroups are: (i) the presence, next to the 5′ splice site, of conserved RNA structures incompatible with the active fold of the group II ribozyme; and (ii) the likely involvement of the ribosome in the facilitation of the splicing process.