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Plant Physiol, January 2003, Vol. 131, pp. 16-26

ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins1

Rainer Schwacke,* Anja Schneider, Eric van der Graaff, Karsten Fischer, Elisabetta Catoni, Marcelo Desimone, Wolf B. Frommer, Ulf-Ingo Flügge, and Reinhard Kunze

Universität zu Köln, Botanisches Institut, Gyrhofstrasse 15, 50931 Köln, Germany (R.S., A.S., E.v.d.G., K.F., U.-I.F., R.K.); and Universität Tübingen, Zentrum für Molekularbiologie der Pflanzen, Auf der Morgenstelle 1, 72076 Tübingen, Germany (E.C., M.D., W.B.F.)

A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.

1 This work was supported by Kleinwanzlebener Saatzacht AG (Einbeck, Germany), by Südzucker AG (Mannheim, Germany), and by the German Ministery for Education and Research-Genomanalyse in biologischen Systemen program.

* Corresponding author; e-mail rainer.schwacke{at}uni-koeln.de; fax 49-221-470 5039.

© 2003 American Society of Plant Biologists


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D. Becker, D. Geiger, M. Dunkel, A. Roller, A. Bertl, A. Latz, A. Carpaneto, P. Dietrich, M. R. G. Roelfsema, C. Voelker, et al.
AtTPK4, an Arabidopsis tandem-pore K+ channel, poised to control the pollen membrane voltage in a pH- and Ca2+-dependent manner
PNAS, November 2, 2004; 101(44): 15621 - 15626.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
R. Swarup, J. Kargul, A. Marchant, D. Zadik, A. Rahman, R. Mills, A. Yemm, S. May, L. Williams, P. Millner, et al.
Structure-Function Analysis of the Presumptive Arabidopsis Auxin Permease AUX1
PLANT CELL, November 1, 2004; 16(11): 3069 - 3083.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
S. Okumoto, W. Koch, M. Tegeder, W. N. Fischer, A. Biehl, D. Leister, Y. D. Stierhof, and W. B. Frommer
Root phloem-specific expression of the plasma membrane amino acid proton co-transporter AAP3
J. Exp. Bot., October 1, 2004; 55(406): 2155 - 2168.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
T. Girke, J. Lauricha, H. Tran, K. Keegstra, and N. Raikhel
The Cell Wall Navigator Database. A Systems-Based Approach to Organism-Unrestricted Mining of Protein Families Involved in Cell Wall Metabolism
Plant Physiology, October 1, 2004; 136(2): 3003 - 3008.
[Full Text] [PDF]

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 J Exp BotHome page
E. Jamet
Bioinformatics as a critical prerequisite to transcriptome and proteome studies
J. Exp. Bot., September 1, 2004; 55(405): 1977 - 1979.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
B. Favery, L. A. Chelysheva, M. Lebris, F. Jammes, A. Marmagne, J. de Almeida-Engler, P. Lecomte, C. Vaury, R. A. Arkowitz, and P. Abad
Arabidopsis Formin AtFH6 Is a Plasma Membrane-Associated Protein Upregulated in Giant Cells Induced by Parasitic Nematodes
PLANT CELL, September 1, 2004; 16(9): 2529 - 2540.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
J. Egelund, M. Skjot, N. Geshi, P. Ulvskov, and B. L. Petersen
A Complementary Bioinformatics Approach to Identify Potential Plant Cell Wall Glycosyltransferase-Encoding Genes
Plant Physiology, September 1, 2004; 136(1): 2609 - 2620.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
A. Marmagne, M.-A. Rouet, M. Ferro, N. Rolland, C. Alcon, J. Joyard, J. Garin, H. Barbier-Brygoo, and G. Ephritikhine
Identification of New Intrinsic Proteins in Arabidopsis Plasma Membrane Proteome
Mol. Cell. Proteomics, July 1, 2004; 3(7): 675 - 691.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
G. Pilot, H. Stransky, D. F. Bushey, R. Pratelli, U. Ludewig, V. P.M. Wingate, and W. B. Frommer
Overexpression of GLUTAMINE DUMPER1 Leads to Hypersecretion of Glutamine from Hydathodes of Arabidopsis Leaves
PLANT CELL, July 1, 2004; 16(7): 1827 - 1840.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
A. P. M. Weber, J. Schneidereit, and L. M. Voll
Using mutants to probe the in vivo function of plastid envelope membrane metabolite transporters
J. Exp. Bot., June 1, 2004; 55(400): 1231 - 1244.
[Abstract] [Full Text] [PDF]

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 J Exp BotHome page
D. Loque and N. von Wiren
Regulatory levels for the transport of ammonium in plant roots
J. Exp. Bot., June 1, 2004; 55(401): 1293 - 1305.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
R. Shingles, L. E. Wimmers, and R. E. McCarty
Copper Transport Across Pea Thylakoid Membranes
Plant Physiology, May 1, 2004; 135(1): 145 - 151.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
A. Rose, S. Manikantan, S. J. Schraegle, M. A. Maloy, E. A. Stahlberg, and I. Meier
Genome-Wide Identification of Arabidopsis Coiled-Coil Proteins and Establishment of the ARABI-COIL Database
Plant Physiology, March 1, 2004; 134(3): 927 - 939.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
F. Samson, V. Brunaud, S. Duchene, Y. De Oliveira, M. Caboche, A. Lecharny, and S. Aubourg
FLAGdb++: a database for the functional analysis of the Arabidopsis genome
Nucleic Acids Res., January 1, 2004; 32(90001): D347 - 350.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
T. Werner, V. Motyka, V. Laucou, R. Smets, H. Van Onckelen, and T. Schmulling
Cytokinin-Deficient Transgenic Arabidopsis Plants Show Multiple Developmental Alterations Indicating Opposite Functions of Cytokinins in the Regulation of Shoot and Root Meristem Activity
PLANT CELL, November 1, 2003; 15(11): 2532 - 2550.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
M. Ferro, D. Salvi, S. Brugiere, S. Miras, S. Kowalski, M. Louwagie, J. Garin, J. Joyard, and N. Rolland
Proteomics of the chloroplast envelope membranes from Arabidopsis thaliana.
Mol. Cell. Proteomics, May 1, 2003; 2(5): 325 - 345.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
S. Knappe, U.-I. Flugge, and K. Fischer
Analysis of the Plastidic phosphate translocator Gene Family in Arabidopsis and Identification of New phosphate translocator-Homologous Transporters, Classified by Their Putative Substrate-Binding Site
Plant Physiology, March 1, 2003; 131(3): 1178 - 1190.
[Abstract] [Full Text] [PDF]


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