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Originally published In Press as doi:10.1074/mcp.M600250-MCP200 on December 6, 2006.
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Molecular & Cellular Proteomics 6:394-412, 2007.
© 2007 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

A Proteomics Dissection of Arabidopsis thaliana Vacuoles Isolated from Cell Culture*,S

Michel Jaquinod{ddagger},§,¶,||,**, Florent Villiers||,{ddagger}{ddagger}, Sylvie Kieffer-Jaquinod{ddagger},§,¶, Véronique Hugouvieux{ddagger}{ddagger}, Christophe Bruley{ddagger},§,¶, Jérôme Garin{ddagger},§,¶ and Jacques Bourguignon{ddagger}{ddagger},§§

From the {ddagger} Laboratoire d’Etude de la dynamique des Protéomes, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), Commissariat à l’Energie Atomique (CEA), § INSERM, ERM 0201, and Université Joseph Fourier, Grenoble F-38054, France and {ddagger}{ddagger} Laboratoire de Physiologie Cellulaire Végétale, UMR 5168, CEA/CNRS/Université Joseph Fourier/Institut National de la Recherche Agronomique (INRA), iRTSV, CEA, CEA-Grenoble, 17 avenue des martyrs, 38054 Grenoble cedex 9, France

To better understand the mechanisms governing cellular traffic, storage of various metabolites, and their ultimate degradation, Arabidopsis thaliana vacuole proteomes were established. To this aim, a procedure was developed to prepare highly purified vacuoles from protoplasts isolated from Arabidopsis cell cultures using Ficoll density gradients. Based on the specific activity of the vacuolar marker {alpha}-mannosidase, the enrichment factor of the vacuoles was estimated at ~42-fold with an average yield of 2.1%. Absence of significant contamination by other cellular compartments was validated by Western blot using antibodies raised against specific markers of chloroplasts, mitochondria, plasma membrane, and endoplasmic reticulum. Based on these results, vacuole preparations showed the necessary degree of purity for proteomics study. Therefore, a proteomics approach was developed to identify the protein components present in both the membrane and soluble fractions of the Arabidopsis cell vacuoles. This approach includes the following: (i) a mild oxidation step leading to the transformation of cysteine residues into cysteic acid and methionine to methionine sulfoxide, (ii) an in-solution proteolytic digestion of very hydrophobic proteins, and (iii) a prefractionation of proteins by short migration by SDS-PAGE followed by analysis by liquid chromatography coupled to tandem mass spectrometry. This procedure allowed the identification of more than 650 proteins, two-thirds of which copurify with the membrane hydrophobic fraction and one-third of which copurifies with the soluble fraction. Among the 416 proteins identified from the membrane fraction, 195 were considered integral membrane proteins based on the presence of one or more predicted transmembrane domains, and 110 transporters and related proteins were identified (91 putative transporters and 19 proteins related to the V-ATPase pump). With regard to function, about 20% of the proteins identified were known previously to be associated with vacuolar activities. The proteins identified are involved in ion and metabolite transport (26%), stress response (9%), signal transduction (7%), and metabolism (6%) or have been described to be involved in typical vacuolar activities, such as protein and sugar hydrolysis. The subcellular localization of several putative vacuolar proteins was confirmed by transient expression of green fluorescent protein fusion constructs.

** To whom correspondence may be addressed: Laboratoire d’Etude de la dynamique des Protéomes, iRTSV, CEA-Grenoble, 17 avenue des martyrs, 38054 Grenoble cedex 9, France. E-mail: jaquinod{at}cea.fr

§§ To whom correspondence may be addressed: Laboratoire de Physiologie Cellulaire Végétale, UMR 5168, CEA/CNRS/Université Joseph Fourier/INRA, iRTSV, CEA-Grenoble, 17 avenue des martyrs, 38054 Grenoble cedex 9, France. E-mail: jacques.bourguignon{at}cea.fr


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