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GENOME ANALYSIS

A Large Complement of the Predicted Arabidopsis ARM Repeat Proteins Are Members of the U-Box E3 Ubiquitin Ligase Family^1,[w]

Department of Botany, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (Y.M., S.L.S., J.N.S., D.R.G.); and Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.-H.S.)

The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins. Using domain database predictions and models generated in this study, 108 Arabidopsis proteins were identified that contained a minimum of two ARM repeats with the majority of proteins containing four to eight ARM repeats. Clustering analysis showed that the 108 predicted Arabidopsis ARM repeat proteins could be divided into multiple groups with wide differences in their domain compositions and organizations. Interestingly, 41 of the 108 Arabidopsis ARM repeat proteins contained a U-box, a motif present in a family of E3 ligases, and these proteins represented the largest class of Arabidopsis ARM repeat proteins. In 14 of these U-box/ARM repeat proteins, there was also a novel conserved domain identified in the N-terminal region. Based on the phylogenetic tree, representative U-box/ARM repeat proteins were selected for further study. RNA-blot analyses revealed that these U-box/ARM proteins are expressed in a variety of tissues in Arabidopsis. In addition, the selected U-box/ARM proteins were found to be functional E3 ubiquitin ligases. Thus, these U-box/ARM proteins represent a new family of E3 ligases in Arabidopsis.

¹ This work was supported by the Natural Sciences and Engineering Research Council of Canada (grant to D.R.G. and graduate scholarship to S.L.S.), by an Ontario Premier's Research in Excellence Award (to D.R.G.), and by the National Institutes of Health (National Research Service Award grant no. 1F32GM066554–01 to S.-H.S.).

^[w] The online version of this article contains Web-only data.

² These authors contributed equally to the paper.

³ Present Address: Section of Molecular and Cellular Biology, Division of Biological Sciences, University of California, Davis, CA 95616.

^* Corresponding author; e-mail goring{at}botany.utoronto.ca; fax 416–978–5878.

Received July 3, 2003; returned for revision August 11, 2003; accepted October 6, 2003.

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