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The Plant Cell, Vol. 14, 211-236, January 2002, Copyright © 2002,
American Society of Plant Biologists

Central Functions of the Lumenal and Peripheral Thylakoid Proteome of Arabidopsis Determined by Experimentation and Genome-Wide Prediction

Jean-Benoît Peltiera, Olof Emanuelssonb,c, Dário E. Kalumed, Jimmy Ytterberga, Giulia Frisoa, Andrea Rudellaa, David A. Liberlesb,c, Linda Söderberg1,b, Peter Roepstorffd, Gunnar von Heijneb,c and Klaas J. van Wijk2,a

a Department of Plant Biology, Cornell University, Ithaca, New York 14853
b Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, S-10691 Stockholm, Sweden
c Stockholm Bioinformatics Center, Stockholm University, S-10691 Stockholm, Sweden
d Department of Molecular Biology, Odense University, DK-5230 Odense M, Denmark

2 To whom correspondence should be addressed. E-mail kv35{at}cornell.edu; fax 1-607-255-5407

Experimental proteome analysis was combined with a genome-wide prediction screen to characterize the protein content of the thylakoid lumen of Arabidopsis chloroplasts. Soluble thylakoid proteins were separated by two-dimensional electrophoresis and identified by mass spectrometry. The identities of 81 proteins were established, and N termini were sequenced to validate localization prediction. Gene annotation of the identified proteins was corrected by experimental data, and an interesting case of alternative splicing was discovered. Expression of a surprising number of paralogs was detected. Expression of five isomerases of different classes suggests strong (un)folding activity in the thylakoid lumen. These isomerases possibly are connected to a network of peripheral and lumenal proteins involved in antioxidative response, including peroxiredoxins, m-type thioredoxins, and a lumenal ascorbate peroxidase. Characteristics of the experimentally identified lumenal proteins and their orthologs were used for a genome-wide prediction of the lumenal proteome. Lumenal proteins with a typical twin-arginine translocation motif were predicted with good accuracy and sensitivity and included additional isomerases and proteases. Thus, prime functions of the lumenal proteome include assistance in the folding and proteolysis of thylakoid proteins as well as protection against oxidative stress. Many of the predicted lumenal proteins must be present at concentrations at least 10,000-fold lower than proteins of the photosynthetic apparatus.




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Y. Fukao, M. Hayashi, I. Hara-Nishimura, and M. Nishimura
Novel Glyoxysomal Protein Kinase, GPK1, Identified by Proteomic Analysis of Glyoxysomes in Etiolated Cotyledons of Arabidopsis thaliana
Plant Cell Physiol., October 15, 2003; 44(10): 1002 - 1012.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
S. M. Gomez, K. Y. Bil', R. Aguilera, J. N. Nishio, K. F. Faull, and J. P. Whitelegge
Transit Peptide Cleavage Sites of Integral Thylakoid Membrane Proteins
Mol. Cell. Proteomics, October 1, 2003; 2(10): 1068 - 1085.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
M. Weigel, C. Varotto, P. Pesaresi, G. Finazzi, F. Rappaport, F. Salamini, and D. Leister
Plastocyanin Is Indispensable for Photosynthetic Electron Flow in Arabidopsis thaliana
J. Biol. Chem., August 15, 2003; 278(33): 31286 - 31289.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
V. Collin, E. Issakidis-Bourguet, C. Marchand, M. Hirasawa, J.-M. Lancelin, D. B. Knaff, and M. Miginiac-Maslow
The Arabidopsis Plastidial Thioredoxins: NEW FUNCTIONS AND NEW INSIGHTS INTO SPECIFICITY
J. Biol. Chem., June 20, 2003; 278(26): 23747 - 23752.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
B. S. Watson, V. S. Asirvatham, L. Wang, and L. W. Sumner
Mapping the Proteome of Barrel Medic (Medicago truncatula)
Plant Physiology, March 1, 2003; 131(3): 1104 - 1123.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
F. Horling, P. Lamkemeyer, J. Konig, I. Finkemeier, A. Kandlbinder, M. Baier, and K.-J. Dietz
Divergent Light-, Ascorbate-, and Oxidative Stress-Dependent Regulation of Expression of the Peroxiredoxin Gene Family in Arabidopsis
Plant Physiology, January 1, 2003; 131(1): 317 - 325.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
A. J.K. Koo and J. B. Ohlrogge
The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles
Plant Physiology, October 1, 2002; 130(2): 823 - 836.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
Y. Chassin, E. Kapri-Pardes, G. Sinvany, T. Arad, and Z. Adam
Expression and Characterization of the Thylakoid Lumen Protease DegP1 from Arabidopsis
Plant Physiology, October 1, 2002; 130(2): 857 - 864.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
D. Alabadi, A. Devoto, and N. A. Eckardt
Arabidopsis Research Heats Up in Seville
PLANT CELL, September 1, 2002; 14(9): 1987 - 1994.
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 Plant Cell PhysiolHome page
Y. Fukao, M. Hayashi, and M. Nishimura
Proteomic Analysis of Leaf Peroxisomal Proteins in Greening Cotyledons of Arabidopsis thaliana
Plant Cell Physiol., July 15, 2002; 43(7): 689 - 696.
[Abstract] [Full Text] [PDF]


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