title: 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.
authors.affiliation: Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Simon
authors.forename: Nicholas A C
authors.initials: NA
authors.lastname: Clarke
authors.forename: Bonnie A
authors.initials: BA
authors.lastname: McNeil
authors.forename: Ian
authors.initials: I
authors.lastname: Johnson
authors.forename: Davin
authors.initials: D
authors.lastname: Pantuso
authors.forename: Lixin
authors.initials: L
authors.lastname: Dai
authors.forename: Dinggeng
authors.initials: D
authors.lastname: Chai
authors.forename: Steven
authors.initials: S
authors.lastname: Zimmerly
mesh_terms: D001105:Archaea / Q000201:enzymology / Q000235:genetics*; D001419:Bacteria / Q000201:enzymology / Q000235:genetics*; D007438:Introns / Q000235:genetics; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D016337:RNA, Catalytic / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D018626:Retroelements
chemical_list: D016337:RNA, Catalytic; D018626:Retroelements