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MBE Advance Access published online on November 2, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj047
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted October 10, 2005

Research Article

Origin and Evolution of the Chloroplast trnK (matK) Intron: a Model for Evolution of Group II Intron RNA Structures

Georg Hausner 1, Robert Olson 2, Dawn Simon 3, Ian Johnson 3, Erin R. Sanders 4, Kenneth G. Karol 5, Richard M. McCourt 6, and Steven Zimmerly 3*

1 Department of Microbiology, Buller Building, University of Manitoba, Winnipeg, Manitoba R3T 2N2 Canada
2 Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4 Canada; Present address: Department of Radiation Oncology, BC Cancer Agency, 600 West 10th Ave., Vancouver, BC V5Z 4E6 Canada
3 Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4 Canada
4 Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1737 USA
5 Department of Biology, 408 Hitchcock Hall, Box 355325, University of Washington, Seattle, WA 98195 USA
6 Department of Botany, Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103 USA

* To whom correspondence should be addressed.
Steven Zimmerly, E-mail: zimmerly{at}ucalgary.ca


  Abstract

The trnK intron of plants encodes the matK ORF, which has been used extensively as a phylogenetic marker for classification of plants. Here we examined the evolution of the trnK intron itself as a model for group II intron evolution in plants. Representative trnK intron sequences were compiled from species spanning algae to angiosperms, and four introns were newly sequenced. Phylogenetic analyses showed that the matK ORFs belong to the ML (mitochondrial-like) subclass of group II intron ORFs, indicating that they were derived from a mobile group II intron of the class. RNA structures of the introns were folded and analyzed, which revealed progressive RNA structural deviations and degenerations throughout plant evolution. The data support a model in which plant organellar group II introns were derived from bacterial-like introns that had "standard" RNA structures and were competent for self-splicing and mobility, and that subsequently the ribozyme structures degenerated to ultimately become dependent upon host splicing factors. We propose that the patterns of RNA structure evolution seen for the trnK intron will apply to other group II introns in plants.


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