Nucleic Acids Research, 2001, Vol. 29, No. 5 1238-1250
© 2001 Oxford University Press
Phylogenetic relationships among group II intron ORFs
Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
Group II introns are widely believed to have been ancestors of spliceosomal introns, yet little is known about their own evolutionary history. In order to address the evolution of mobile group II introns, we have compiled 71 open reading frames (ORFs) related to group II intron reverse transcriptases and subjected their derived amino acid sequences to phylogenetic analysis. The phylogenetic tree was rooted with reverse transcriptases (RTs) of non-long terminal repeat retroelements, and the inferred phylogeny reveals two major clusters which we term the mitochondrial and chloroplast-like lineages. Bacterial ORFs are mainly positioned at the bases of the two lineages but with weak bootstrap support. The data give an overview of an apparently high degree of horizontal transfer of group II intron ORFs, mostly among related organisms but also between organelles and bacteria. The Zn domain (nuclease) and YADD motif (RT active site) were lost multiple times during evolution. Differences in domain structures suggest that the oldest ORFs were concise, while the ORF in the mitochondrial lineage subsequently expanded in three locations. The data are consistent with a bacterial origin for mobile group II introns.
* To whom correspondence should be addressed. Tel: +1 403 220 7933; Fax: +1 403 289 9311; Email: zimmerly{at}ucalgary.ca Present addresses: Georg Hausner, Department of Botany, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada Xu-chu Wu, Department of Cell Biology and Anatomy, University of Calgary School of Medicine, Calgary, Alberta T2N 4N1, Canada
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