Group II introns in Eubacteria and Archaea: ORF-less introns and new varieties
Abstract
Group II introns are a major class of ribozymes found in bacteria, mitochondria, and plastids. Many introns contain reverse transcriptase open reading frames (ORFs) that confer mobility to the introns and allow them to persist as selfish DNAs. Here, we report an updated compilation of group II introns in Eubacteria and Archaea comprising 234 introns. One new phylogenetic class is identified, as well as several specialized lineages. In addition, we undertake a detailed search for ORF-less group II introns in bacterial genomes in order to find undiscovered introns that either entirely lack an ORF or encode a novel ORF. Unlike organellar group II introns, we find only a handful of ORF-less introns in bacteria, suggesting that if a substantial number exist, they must be divergent from known introns. Together, these results highlight the retroelement character of bacterial group II introns, and suggest that their long-term survival is dependent upon retromobility.
Keywords
Footnotes
-
↵1 Present addresses: Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
-
↵2 Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
-
Reprint requests to: Steven Zimmerly; Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada; e-mail: zimmerly{at}ucalgary.ca; fax: (403) 289-9311.
-
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.1056108.
-
- Received March 11, 2008.
- Accepted June 3, 2008.
- Copyright © 2008 RNA Society
