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Molecular & Cellular Proteomics 4:1072-1084, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Proteome Analysis of the Rice Etioplast

Metabolic and Regulatory Networks and Novel Protein Functions^*,S

Anne von Zychlinski^,,¶, Torsten Kleffmann^,,||, Nandini Krishnamurthy^**, Kimmen Sjölander^**, Sacha Baginsky^, and Wilhelm Gruissem

From the Institute of Plant Science and Functional Genomics Center Zurich, Swiss Federal Institute of Technology, Eidgenössische Technische Hochschule (ETH) Zurich, 8092 Zurich, Switzerland and the ^** Department of Bioengineering, University of California, Berkeley, California 94720

We report an extensive proteome analysis of rice etioplasts, which were highly purified from dark-grown leaves by a novel protocol using Nycodenz density gradient centrifugation. Comparative protein profiling of different cell compartments from leaf tissue demonstrated the purity of the etioplast preparation by the absence of diagnostic marker proteins of other cell compartments. Systematic analysis of the etioplast proteome identified 240 unique proteins that provide new insights into heterotrophic plant metabolism and control of gene expression. They include several new proteins that were not previously known to localize to plastids. The etioplast proteins were compared with proteomes from Arabidopsis chloroplasts and plastid from tobacco Bright Yellow 2 cells. Together with computational structure analyses of proteins without functional annotations, this comparative proteome analysis revealed novel etioplast-specific proteins. These include components of the plastid gene expression machinery such as two RNA helicases, an RNase II-like hydrolytic exonuclease, and a site 2 protease-like metalloprotease all of which were not known previously to localize to the plastid and are indicative for so far unknown regulatory mechanisms of plastid gene expression. All etioplast protein identifications and related data were integrated into a data base that is freely available upon request.

To whom correspondence may be addressed: Inst. of Plant Sciences, Swiss Federal Inst. of Technology, ETH Zentrum, LFW E51.1, Universitätstrasse 2, CH-8092 Zürich, Switzerland. Tel.: 41-1-632-3866; Fax: 41-1-632-10-79; E-mail: sacha.baginsky{at}ipw.biol.ethz.ch

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