Open Access Research article

Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns

Peik Haugen16*, Debashish Bhattacharya1, Jeffrey D Palmer2, Seán Turner3, Louise A Lewis4 and Kathleen M Pryer5

Author Affiliations

1 Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, IA 52242, USA

2 Department of Biology, Indiana University, Bloomington, IN 47405, USA

3 National Center for Biotechnology Information, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, MD 20892, USA

4 Department of Ecology and Evolutionary Biology, The University of Connecticut, Storrs, CT 06269, USA

5 Department of Biology, Duke University, Durham, NC 27708, USA

6 Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway

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BMC Evolutionary Biology 2007, 7:159  doi:10.1186/1471-2148-7-159

Published: 8 September 2007



Group I introns are one of the four major classes of introns as defined by their distinct splicing mechanisms. Because they catalyze their own removal from precursor transcripts, group I introns are referred to as autocatalytic introns. Group I introns are common in fungal and protist nuclear ribosomal RNA genes and in organellar genomes. In contrast, they are rare in all other organisms and genomes, including bacteria.


Here we report five group I introns, each containing a LAGLIDADG homing endonuclease gene (HEG), in large subunit (LSU) rRNA genes of cyanobacteria. Three of the introns are located in the LSU gene of Synechococcus sp. C9, and the other two are in the LSU gene of Synechococcus lividus strain C1. Phylogenetic analyses show that these introns and their HEGs are closely related to introns and HEGs located at homologous insertion sites in organellar and bacterial rDNA genes. We also present a compilation of group I introns with homing endonuclease genes in bacteria.


We have discovered multiple HEG-containing group I introns in a single bacterial gene. To our knowledge, these are the first cases of multiple group I introns in the same bacterial gene (multiple group I introns have been reported in at least one phage gene and one prophage gene). The HEGs each contain one copy of the LAGLIDADG motif and presumably function as homodimers. Phylogenetic analysis, in conjunction with their patchy taxonomic distribution, suggests that these intron-HEG elements have been transferred horizontally among organelles and bacteria. However, the mode of transfer and the nature of the biological connections among the intron-containing organisms are unknown.