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Functional Hammerhead Ribozymes Naturally Encoded in the Genome of Arabidopsis thaliana

^a Arbeitsgruppe Molecular Interactions, Department of Genetics, Universität Kassel, D-34132 Kassel, Germany
^b Institut für Physikalische Biologie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
^c Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, F-67084 Strasbourg Cedex, France
^d Department of Genetics, Universität Kassel, D-34132 Kassel, Germany

² To whom correspondence should be addressed. E-mail c.hammann{at}uni-kassel.de; fax 49-561-804-4800.

The hammerhead ribozyme (HHRz) is an autocatalytic RNA motif found in subviral plant pathogens and transcripts of repetitive DNA sequences in animals. Here, we report the discovery and characterization of unique HHRzs encoded in a plant genome. Two novel sequences were identified on chromosome IV of Arabidopsis thaliana in a database search, which took into account recently defined structural requirements. The HHRzs are expressed in several tissues and coexist in vivo as both cleaved and noncleaved species. In vitro, both sequences cleave efficiently at physiological Mg²⁺ concentrations, indicative of functional loop–loop interactions. Kinetic analysis of loop nucleotide variants was used to determine a three-dimensional model of these tertiary interactions. Based on these results, on the lack of infectivity of hammerhead-carrying viroids in Arabidopsis, and on extensive sequence comparisons, we propose that the ribozyme sequences did not invade this plant by horizontal transfer but have evolved independently to perform a specific, yet unidentified, biological function.

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