Functional Hammerhead Ribozymes Naturally Encoded in the Genome of Arabidopsis thaliana

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...

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Bibliographic Details
Published in:The Plant cell 2005-07, Vol.17 (7), p.1877-1885
Main Authors: Przybilski, Rita, Gräf, Stefan, Lescoute, Aurélie, Nellen, Wolfgang, Westhof, Eric, Steger, Gerhard, Hammann, Christian
Format: Article
Language:English
Subjects:
Antisense RNA
Arabidopsis - genetics
Arabidopsis - metabolism
Arabidopsis - virology
Arabidopsis thaliana
autocatalytic RNA
Base Sequence - genetics
Complementary DNA
DNA
Gene Expression Regulation, Plant - genetics
genes
genome
Genome, Plant
Genomes
hammerhead ribozymes
Magnesium - metabolism
Models, Molecular
molecular conformation
nucleotide sequences
Nucleotides
Nucleotides - genetics
Polymerase chain reaction
Reverse transcriptase polymerase chain reaction
RNA
RNA, Catalytic - genetics
RNA, Plant - genetics
Viroids
Viroids - genetics
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Summary: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.
ISSN:1040-4651
1532-298X
1532-298X
DOI:10.1105/tpc.105.032730