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Plant Physiology 137:13-30 (2005)
© 2005 American Society of Plant Biologists

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GENOME ANALYSIS

Functional Analysis of the RING-Type Ubiquitin Ligase Family of Arabidopsis1,[w]

Sophia L. Stone, Herborg Hauksdóttir2, Andrew Troy, Jill Herschleb3, Edward Kraft and Judy Callis*

Section of Molecular and Cellular Biology, Division of Biological Sciences (S.L.S., H.H., A.T., J.H., E.K., J.C.), and Plant Biology Graduate Group Program (E.K., J.C.), University of California, Davis, California 95616

Approximately 5% of the Arabidopsis (Arabidopsis thaliana) proteome is predicted to be involved in the ubiquitination/26S proteasome pathway. The majority of these predicted proteins have identity to conserved domains found in E3 ligases, of which there are multiple types. The RING-type E3 is characterized by the presence of a cysteine-rich domain that coordinates two zinc atoms. Database searches followed by extensive manual curation identified 469 predicted Arabidopsis RING domain-containing proteins. In addition to the two canonical RING types (C3H2C3 or C3HC4), additional types of modified RING domains, named RING-v, RING-D, RING-S/T, RING-G, and RING-C2, were identified. The modified RINGs differ in either the spacing between metal ligands or have substitutions at one or more of the metal ligand positions. The majority of the canonical and modified RING domain-containing proteins analyzed were active in in vitro ubiquitination assays, catalyzing polyubiquitination with the E2 AtUBC8. To help identity regions of the proteins that may interact with substrates, domain analyses of the amino acids outside the RING domain classified RING proteins into 30 different groups. Several characterized protein-protein interaction domains were identified, as well as additional conserved domains not described previously. The two largest classes of RING proteins contain either no identifiable domain or a transmembrane domain. The presence of such a large and diverse number of RING domain-containing proteins that function as ubiquitin E3 ligases suggests that target-specific proteolysis by these E3 ligases is a complex and important part of cellular regulation in Arabidopsis.

1 This work was supported by the National Science Foundation (2010 grant no. MCB–00115870). E.K. also was partially supported by the National Institute of Health Training (grant no. GM0007377–27), and S.L.S. was supported by the Natural Sciences and Engineering Research Council of Canada and the International Human Frontier Science Program fellowships.

2 Present address: Molecular Biology Laboratory, Institute for Experimental Pathology, University of Iceland, Keldur, v/Vesturlandsveg, IS-112 Reykjavik, Iceland.

3 Present address: Laboratory for Molecular and Computational Genomics, UW Biotechnology Center, Madison, WI 53706.

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

www.plantphysiol.org/cgi/doi/10.1104/pp.104.052423.

* Corresponding author; e-mail jcallis{at}ucdavis.edu; fax 530–752–3085.

Received August 25, 2004; returned for revision November 2, 2004; accepted November 10, 2004.




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