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Plant Cell, Vol. 12, 319-342, March 2000, Copyright © 2000, American Society of Plant Physiologists

Proteomics of the Chloroplast: Systematic Identification and Targeting Analysis of Lumenal and Peripheral Thylakoid Proteins

Jean-Benoît Peltiera, Giulia Frisob, Dário Eluan Kalumec, Peter Roepstorffc, Frederik Nilssond, Iwona Adamskaa, and Klaas J. van Wijka
a Department of Biochemistry, Arrhenius Laboratories, Stockholm University, S-10691 Stockholm, Sweden
b Department of Cellular and Molecular Pharmacology, AstraZeneca Novum, S-14157 Huddinge, Sweden
c Department of Molecular Biology, Odense University, DK-5230 Odense M, Denmark
d Department of Bioanalytical Chemistry, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden

Correspondence to: Klaas J. van Wijk, klaas{at}biokemi.su.se (E-mail), 46-8-153679 (fax)

The soluble and peripheral proteins in the thylakoids of pea were systematically analyzed by using two-dimensional electrophoresis, mass spectrometry, and N-terminal Edman sequencing, followed by database searching. After correcting to eliminate possible isoforms and post-translational modifications, we estimated that there are at least 200 to 230 different lumenal and peripheral proteins. Sixty-one proteins were identified; for 33 of these proteins, a clear function or functional domain could be identified, whereas for 10 proteins, no function could be assigned. For 18 proteins, no expressed sequence tag or full-length gene could be identified in the databases, despite experimental determination of a significant amount of amino acid sequence. Nine previously unidentified proteins with lumenal transit peptides are presented along with their full-length genes; seven of these proteins possess the twin arginine motif that is characteristic for substrates of the TAT pathway. Logoplots were used to provide a detailed analysis of the lumenal targeting signals, and all nuclear-encoded proteins identified on the two-dimensional gels were used to test predictions for chloroplast localization and transit peptides made by the software programs ChloroP, PSORT, and SignalP. A combination of these three programs was found to provide a useful tool for evaluating chloroplast localization and transit peptides and also could reveal possible alternative processing sites and dual targeting. The potential of proteomics for plant biology and homology-based searching with mass spectrometry data is discussed.


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