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GENOME ANALYSIS

Glycosylphosphatidylinositol Lipid Anchoring of Plant Proteins. Sensitive Prediction from Sequence- and Genome-Wide Studies for Arabidopsis and Rice¹

Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A–1030 Vienna, Austria (B.E., M.W., F.E.); School of Agriculture and Wine, Waite Agriculture Research Institute, The University of Adelaide, RMB1, Glen Osmond, South Australia 5064, Australia (C.J.S.); and University of Cambridge, Department of Biochemistry, Cambridge Centre for Proteomics, Cambridge CB2 1QW, United Kingdom (G.H.H.B., P.D.)

Posttranslational glycosylphosphatidylinositol (GPI) lipid anchoring is common not only for animal and fungal but also for plant proteins. The attachment of the GPI moiety to the carboxyl-terminus after proteolytic cleavage of a C-terminal propeptide is performed by the transamidase complex. Its four known subunits also have obvious full-length orthologs in the Arabidopsis and rice (Oryza sativa) genomes; thus, the mechanism of substrate protein processing appears similar for all eukaryotes. A learning set of plant proteins (substrates for the transamidase complex) has been collected both from the literature and plant sequence databases. We find that the plant GPI lipid anchor motif differs in minor aspects from the animal signal (e.g. the plant hydrophobic tail region can contain a higher fraction of aromatic residues). We have developed the "big- plant" program for prediction of compatibility of query protein C-termini with the plant GPI lipid anchor motif requirements. Validation tests show that the sensitivity for transamidase targets is approximately 94%, and the rate of false positive prediction is about 0.1%. Thus, the big- predictor can be applied as unsupervised genome annotation and target selection tool. The program is also suited for the design of modified protein constructs to test their GPI lipid anchoring capacity. The big- plant predictor Web server and lists of potential plant precursor proteins in Swiss-Prot, SPTrEMBL, Arabidopsis, and rice proteomes are available at http://mendel.imp.univie.ac.at/gpi/plants/gpi_plants.html. Arabidopsis and rice protein hits have been functionally classified. Several GPI lipid-anchored arabinogalactan-related proteins have been identified in rice.

¹ This work was supported by the Boehringer Ingelheim (continuous support to B.E., M.W., and F.E.), in part by the Fonds zur Förderung der Wissenschaftlichen Forschung Österreichs (grant no. FWF P15037), by the Austrian National Bank (Österreichische Nationalbank), by the Austrian Ministry of Economic Affairs (BMWA), by the Austrian Gen-AU Program (bioinformatics integration network grant), by the Australian Research Council (Discovery grant no. DP0343454 to C.S.), by the University of Adelaide (partial support for a visit to Vienna for this project), by the Biotechnology and Biological Sciences Research Council (research studentship to G.H.H.B.), and by the Studienstiftung des Deutschen Volkes (scholarship to G.H.H.B.).

^* Corresponding author; e-mail Birgit.Eisenhaber{at}imp.univie.ac.at; fax 43–1–7987–153.

Received March 27, 2003; returned for revision June 27, 2003; accepted August 21, 2003.

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