First published online April 25, 2002; 10.1104/pp.010884
Plant Physiol, June 2002, Vol. 129, pp. 486-499
Prediction of Glycosylphosphatidylinositol-Anchored Proteins in
Arabidopsis. A Genomic Analysis1
Georg H.H.
Borner,
D. Janine
Sherrier,2
Timothy J.
Stevens,
Isaiah T.
Arkin,3 and
Paul
Dupree*
Department of Biochemistry, University of Cambridge, Cambridge, CB2
1QW, United Kingdom
Glycosylphosphatidylinositol (GPI) anchoring of proteins
provides a potential mechanism for targeting to the plant plasma membrane and cell wall. However, relatively few such proteins have been
identified. Here, we develop a procedure for database analysis to
identify GPI-anchored proteins (GAP) based on their possession of
common features. In a comprehensive search of the annotated Arabidopsis
genome, we identified 167 novel putative GAP in addition to the 43 previously described candidates. Many of these 210 proteins show
similarity to characterized cell surface proteins. The predicted GAP
include homologs of  -1,3-glucanases (16), metallo- and aspartyl
proteases (13), glycerophosphodiesterases (6), phytocyanins (25),
multi-copper oxidases (2), extensins (6), plasma membrane receptors
(19), and lipid-transfer-proteins (18). Classical arabinogalactan (AG)
proteins (13), AG peptides (9), fasciclin-like proteins (20), COBRA and
10 homologs, and novel potential signaling peptides that we name GAPEPs
(8) were also identified. A further 34 proteins of unknown function
were predicted to be GPI anchored. A surprising finding was that over
40% of the proteins identified here have probable AG glycosylation
modules, suggesting that AG glycosylation of cell surface proteins is
widespread. This analysis shows that GPI anchoring is likely to be a
major modification in plants that is used to target a specific subset of proteins to the cell surface for extracellular matrix remodeling and signaling.
1
This work was supported by the
Biotechnology and Biological Sciences Research Council and by the
European Commission. G.H.H.B. also received a scholarship from the
Studienstiftung des Deutschen Volkes.
2
Present address: Department of Plant and Soil Sciences
and Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19717.
3
Present address: Hebrew University Jerusalem, Department
of Biological Chemistry, Alexander Silberman Institute of Life
Sciences, Givat Ram, IL-91904 Jerusalem, Israel.
*
Corresponding author; e-mail p.dupree{at}bioc.cam.ac.uk; fax
44-1223-333345.
© 2002 American Society of Plant Physiologists
This article has been cited by other articles:
|
|
|
|
 
A. Marmagne, M. Ferro, T. Meinnel, C. Bruley, L. Kuhn, J. Garin, H. Barbier-Brygoo, and G. Ephritikhine
A High Content in Lipid-modified Peripheral Proteins and Integral Receptor Kinases Features in the Arabidopsis Plasma Membrane Proteome
Mol. Cell. Proteomics,
November 1, 2007;
6(11):
1980 - 1996.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. C. Doxey, M. W. F. Yaish, B. A. Moffatt, M. Griffith, and B. J. McConkey
Functional Divergence in the Arabidopsis {beta}-1,3-Glucanase Gene Family Inferred by Phylogenetic Reconstruction of Expression States
Mol. Biol. Evol.,
April 1, 2007;
24(4):
1045 - 1055.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. A. Khan, Q. Wang, R. D. Sjolund, A. Schulz, and G. A. Thompson
An Early Nodulin-Like Protein Accumulates in the Sieve Element Plasma Membrane of Arabidopsis
Plant Physiology,
April 1, 2007;
143(4):
1576 - 1589.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. K. Grennan
Lipid Rafts in Plants
Plant Physiology,
March 1, 2007;
143(3):
1083 - 1085.
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. L. Richard and A. Plaine
Comprehensive Analysis of Glycosylphosphatidylinositol-Anchored Proteins in Candida albicans
Eukaryot. Cell,
February 1, 2007;
6(2):
119 - 133.
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. M. Estevez, M. J. Kieliszewski, N. Khitrov, and C. Somerville
Characterization of Synthetic Hydroxyproline-Rich Proteoglycans with Arabinogalactan Protein and Extensin Motifs in Arabidopsis
Plant Physiology,
October 1, 2006;
142(2):
458 - 470.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J.-H. Ko, J. H. Kim, S. S. Jayanty, G. A. Howe, and K.-H. Han
Loss of function of COBRA, a determinant of oriented cell expansion, invokes cellular defence responses in Arabidopsis thaliana
J. Exp. Bot.,
September 1, 2006;
57(12):
2923 - 2936.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Ichinose, A. Kuno, T. Kotake, M. Yoshida, K. Sakka, J. Hirabayashi, Y. Tsumuraya, and S. Kaneko
Characterization of an Exo-{beta}-1,3-Galactanase from Clostridium thermocellum.
Appl. Envir. Microbiol.,
May 1, 2006;
72(5):
3515 - 3523.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. J. Kwon, E. Y. Choi, Y. J. Choi, J. H. Ahn, and O. K Park
Proteomics studies of post-translational modifications in plants
J. Exp. Bot.,
April 1, 2006;
57(7):
1547 - 1551.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
W. Sun, J. Xu, J. Yang, M. J. Kieliszewski, and A. M. Showalter
The Lysine-rich Arabinogalactan-protein Subfamily in Arabidopsis: Gene Expression, Glycoprotein Purification and Biochemical Characterization
Plant Cell Physiol.,
June 1, 2005;
46(6):
975 - 984.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. C. Peck
Update on Proteomics in Arabidopsis. Where Do We Go From Here?
Plant Physiology,
June 1, 2005;
138(2):
591 - 599.
[Full Text]
[PDF]
|
|
|
|
|
|
|
F. Roudier, A. G. Fernandez, M. Fujita, R. Himmelspach, G. H.H. Borner, G. Schindelman, S. Song, T. I. Baskin, P. Dupree, G. O. Wasteneys, et al.
COBRA, an Arabidopsis Extracellular Glycosyl-Phosphatidyl Inositol-Anchored Protein, Specifically Controls Highly Anisotropic Expansion through Its Involvement in Cellulose Microfibril Orientation
PLANT CELL,
June 1, 2005;
17(6):
1749 - 1763.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C. S. Gillmor, W. Lukowitz, G. Brininstool, J. C. Sedbrook, T. Hamann, P. Poindexter, and C. Somerville
Glycosylphosphatidylinositol-Anchored Proteins Are Required for Cell Wall Synthesis and Morphogenesis in Arabidopsis
PLANT CELL,
April 1, 2005;
17(4):
1128 - 1140.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Aspeborg, J. Schrader, P. M. Coutinho, M. Stam, A. Kallas, S. Djerbi, P. Nilsson, S. Denman, B. Amini, F. Sterky, et al.
Carbohydrate-Active Enzymes Involved in the Secondary Cell Wall Biogenesis in Hybrid Aspen
Plant Physiology,
March 1, 2005;
137(3):
983 - 997.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
G. H.H. Borner, D. J. Sherrier, T. Weimar, L. V. Michaelson, N. D. Hawkins, A. MacAskill, J. A. Napier, M. H. Beale, K. S. Lilley, and P. Dupree
Analysis of Detergent-Resistant Membranes in Arabidopsis. Evidence for Plasma Membrane Lipid Rafts
Plant Physiology,
January 1, 2005;
137(1):
104 - 116.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
E. Alexandersson, G. Saalbach, C. Larsson, and P. Kjellbom
Arabidopsis Plasma Membrane Proteomics Identifies Components of Transport, Signal Transduction and Membrane Trafficking
Plant Cell Physiol.,
November 15, 2004;
45(11):
1543 - 1556.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C. J. Schultz, K. L. Ferguson, J. Lahnstein, and A. Bacic
Post-translational Modifications of Arabinogalactan-peptides of Arabidopsis thaliana: ENDOPLASMIC RETICULUM AND GLYCOSYLPHOSPHATIDYLINOSITOL-ANCHOR SIGNAL CLEAVAGE SITES AND HYDROXYLATION OF PROLINE
J. Biol. Chem.,
October 29, 2004;
279(44):
45503 - 45511.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
G. Acosta-Garcia and J.-P. Vielle-Calzada
A Classical Arabinogalactan Protein Is Essential for the Initiation of Female Gametogenesis in Arabidopsis
PLANT CELL,
October 1, 2004;
16(10):
2614 - 2628.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. M. Gaspar, J. Nam, C. J. Schultz, L.-Y. Lee, P. R. Gilson, S. B. Gelvin, and A. Bacic
Characterization of the Arabidopsis Lysine-Rich Arabinogalactan-Protein AtAGP17 Mutant (rat1) That Results in a Decreased Efficiency of Agrobacterium Transformation
Plant Physiology,
August 1, 2004;
135(4):
2162 - 2171.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
E. Lalanne, D. Honys, A. Johnson, G. H. H. Borner, K. S. Lilley, P. Dupree, U. Grossniklaus, and D. Twell
SETH1 and SETH2, Two Components of the Glycosylphosphatidylinositol Anchor Biosynthetic Pathway, Are Required for Pollen Germination and Tube Growth in Arabidopsis
PLANT CELL,
January 1, 2004;
16(1):
229 - 240.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
F. Elortza, T. S. Nuhse, L. J. Foster, A. Stensballe, S. C. Peck, and O. N. Jensen
Proteomic Analysis of Glycosylphosphatidylinositol-anchored Membrane Proteins
Mol. Cell. Proteomics,
December 1, 2003;
2(12):
1261 - 1270.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
B. Eisenhaber, M. Wildpaner, C. J. Schultz, G. H.H. Borner, P. Dupree, and F. Eisenhaber
Glycosylphosphatidylinositol Lipid Anchoring of Plant Proteins. Sensitive Prediction from Sequence- and Genome-Wide Studies for Arabidopsis and Rice
Plant Physiology,
December 1, 2003;
133(4):
1691 - 1701.
[Abstract]
[Full Text]
|
|
|
|
|
|
|
K. L. Johnson, B. J. Jones, A. Bacic, and C. J. Schultz
The Fasciclin-Like Arabinogalactan Proteins of Arabidopsis. A Multigene Family of Putative Cell Adhesion Molecules
Plant Physiology,
December 1, 2003;
133(4):
1911 - 1925.
[Abstract]
[Full Text]
|
|
|
|
|
|
|
F. Baluska, J. Samaj, P. Wojtaszek, D. Volkmann, and D. Menzel
Cytoskeleton-Plasma Membrane-Cell Wall Continuum in Plants. Emerging Links Revisited
Plant Physiology,
October 1, 2003;
133(2):
482 - 491.
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. D. Becker, L. C. Boavida, J. Carneiro, M. Haury, and J. A. Feijo
Transcriptional Profiling of Arabidopsis Tissues Reveals the Unique Characteristics of the Pollen Transcriptome
Plant Physiology,
October 1, 2003;
133(2):
713 - 725.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
L. Tan, J. F. Leykam, and M. J. Kieliszewski
Glycosylation Motifs That Direct Arabinogalactan Addition to Arabinogalactan-Proteins
Plant Physiology,
July 1, 2003;
132(3):
1362 - 1369.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
G. H.H. Borner, K. S. Lilley, T. J. Stevens, and P. Dupree
Identification of Glycosylphosphatidylinositol-Anchored Proteins in Arabidopsis. A Proteomic and Genomic Analysis
Plant Physiology,
June 1, 2003;
132(2):
568 - 577.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
G. Breton, J. Danyluk, J.-B. F. Charron, and F. Sarhan
Expression Profiling and Bioinformatic Analyses of a Novel Stress-Regulated Multispanning Transmembrane Protein Family from Cereals and Arabidopsis
Plant Physiology,
May 1, 2003;
132(1):
64 - 74.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
F. Goubet, A. Misrahi, S. K. Park, Z. Zhang, D. Twell, and P. Dupree
AtCSLA7, a Cellulose Synthase-Like Putative Glycosyltransferase, Is Important for Pollen Tube Growth and Embryogenesis in Arabidopsis
Plant Physiology,
February 1, 2003;
131(2):
547 - 557.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Zik and V. F. Irish
Global Identification of Target Genes Regulated by APETALA3 and PISTILLATA Floral Homeotic Gene Action
PLANT CELL,
January 1, 2003;
15(1):
207 - 222.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. C. Sedbrook, K. L. Carroll, K. F. Hung, P. H. Masson, and C. R. Somerville
The Arabidopsis SKU5 Gene Encodes an Extracellular Glycosyl Phosphatidylinositol-Anchored Glycoprotein Involved in Directional Root Growth
PLANT CELL,
July 1, 2002;
14(7):
1635 - 1648.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
